Investigation of petabyte-scale data transfer performances with PhEDEx for the CMS experiment

PhEDEx, the CMS transfer management system, during the first LHC Run has moved about 150 PB and currently it is moving about 2.5 PB of data per week over the Worldwide LHC Computing Grid (WLGC). It was designed to complete each transfer required by users at the expense of the waiting time necessary for its completion. For this reason, after several years of operations, data regarding transfer latencies has been collected and stored into log files containing useful analyzable informations. Then, starting from the analysis of several typical CMS transfer workflows, a categorization of such latencies has been made with a focus on the different factors that contribute to the transfer completion time. The analysis presented in this thesis will provide the necessary information for equipping PhEDEx in the future with a set of new tools in order to proactively identify and fix any latency issues. PhEDEx, il sistema di gestione dei trasferimenti di CMS, durante il primo Run di LHC ha trasferito all’incirca 150 PB ed attualmente trasferisce circa 2.5 PB di dati alla settimana attraverso la Worldwide LHC Computing Grid (WLCG). Questo sistema è stato progettato per completare ogni trasferimento richiesto dall’utente a spese del tempo necessario per il suo completamento. Dopo svariati anni di operazioni con tale strumento, sono stati raccolti dati relativi alle latenze di trasferimento ed immagazzinati in log files contenenti informazioni utili per l’analisi. A questo punto, partendo dall’analisi di una ampia mole di trasferimenti in CMS, è stata effettuata una suddivisione di queste latenze ponendo particolare attenzione nei confronti dei fattori che contribuiscono al tempo di completamento del trasferimento. L’analisi presentata in questa tesi permetterà di equipaggiare PhEDEx con un insieme di utili strumenti in modo tale da identificare proattivamente queste latenze e adottare le opportune tattiche per minimizzare l’impatto sugli utenti finali.

Gender inequity in the provision of care for hip disease: population-based cross-sectional study

Objectives To examine gender differences along the care pathway to total hip replacement. Methods We conducted a population-based cross-sectional study of 26,046 individuals aged 35 years and over in Avon and Somerset. Participants completed a questionnaire asking about care provision at five milestones on the pathway to total hip replacement. Those reporting hip disease were invited to a clinical examination. We estimated odds ratios (ORs) [95% confidence intervals (CI)] for provision of care to women compared with men. Results 3169 people reported hip pain, 2018 were invited for clinical examination, and 1405 attended (69.6%). After adjustment for age and disease severity, women were less likely than men to have consulted their general practitioner (OR 0.78, 95%-CI 0.61–1.00), as likely as men to have received drug therapy for hip pain in the previous year (OR 0.96, 95%-CI 0.74–1.24), but less likely to have been referred to specialist care (OR 0.53, 95%-CI 0.40–0.70), to have consulted an orthopaedic surgeon (OR 0.50, 95%-CI 0.32–0.78), or to be on a waiting list for total hip replacement (OR 0.41, 95%-CI 0.20–0.87). Differences remained in the 746 people who had sought care from their general practitioner, and after adjustment for willingness and fitness for surgery. Conclusions There are gender inequalities in provision of care for hip disease in England, which are not fully accounted for by gender differences in care seeking and treatment preferences. Differences in referral to specialist care by general practitioners might unwittingly contribute to this inequity. Accurate information about availability, benefits and risks of hip replacement for providers and patients, and continuing education to ensure that clinicians interpret and correct patients' assumptions could help reduce inequalities.

Dialysis and Renal Transplantation in HIV-Infected Patients: a European Survey

OBJECTIVES:: To determine prevalence and characteristics of end-stage renal diseases (ESRD) [dialysis and renal transplantation (RT)] among European HIV-infected patients. METHODS:: Cross-sectional multicenter survey of EuroSIDA clinics during 2008. RESULTS:: Prevalence of ESRD was 0.5%. Of 122 patients with ESRD 96 were on dialysis and 26 had received a RT. Median age was 47 years, 73% were males and 43% were black. Median duration of HIV infection was 11 years. Thirty-three percent had prior AIDS; 91% were receiving antiretrovirals; and 88% had undetectable viral load. Median CD4T-cell count was 341 cells per cubic millimetre; 20.5% had hepatitis C coinfection. Most frequent causes of ESRD were HIV-associated nephropathy (46%) and other glomerulonephritis (28%). Hemodialysis (93%) was the most common dialysis modality; 34% of patients were on the RT waiting list. A poor HIV control was the reason for exclusion from RT waiting list in 22.4% of cases. All the RT recipients were all alive at the time of the survey. Acute rejection was reported in 8 patients (30%). Functioning graft was present in 21 (80%). CONCLUSIONS:: This is the first multinational cross-sectional study of ESRD among European HIV population. Low prevalence of ESRD was found. Two-thirds of patients were excluded from RT for non-HIV/AIDS-related pathologies. Most patients had a functioning graft despite a high acute rejection rate.

Immediate Search in the IDE as an Example of Socio-Technical Congruence in Search-Driven Development

Search-driven development is mainly concerned with code reuse but also with code navigation and debugging. In this essay we look at search-driven navigation in the IDE. We consider Smalltalk-80 as an example of a programming system with search-driven navigation capabilities and explore its human factors. We present how immediate search results lead to a user experience of code browsing rather than one of waiting for and clicking through search results. We explore the socio-technical congruence of immediate search, ie unification of tasks and breakpoints with method calls, which leads to simpler and more extensible development tools. Eventually we conclude with remarks on the socio-technical congruence of search-driven development.

Microscopic Picture of Aging in SiO2

We investigate the aging dynamics of amorphous SiO2 via molecular dynamics simulations of a quench from a high temperature Ti to a lower temperature Tf.We obtain a microscopic picture of aging dynamics by analyzing single particle trajectories, identifying jump events when a particle escapes the cage formed by its neighbors, and determining how these jumps depend on the waiting time tw, the time elapsed since the temperature quench to Tf. We find that the only tw-dependent microscopic quantity is the number of jumping particles per unit time, which decreases with age. Similar to previous studies for fragile glass formers, we show here for the strong glass former SiO2 that neither the distribution of jump lengths nor the distribution of times spent in the cage are tw dependent.We conclude that the microscopic aging dynamics is surprisingly similar for fragile and strong glass formers.

The efficacy of non-directive supportive therapy for adult depression: A meta-analysis

The effects of non-directive supportive therapy (NDST) for adult depression have been examined in a considerable number of studies, but no meta-analysis of these studies has been conducted. We selected 31 studies on NDST from a comprehensive database of trials, examining psychotherapies for adult depression, and conducted meta-analyses in which NDST was compared with control groups, other psychotherapies and pharmacotherapy. We found that NDST is effective in the treatment of depression in adults (g=0.58; 95% CI: 0.45-0.72). NDST was less effective than other psychological treatments (differential effect size g=-0.20; 95% CI: -0.32 to -0.08, p<0.01), but these differences were no longer present after controlling for researcher allegiance. We estimated that extra-therapeutic factors (those processes operating in waiting-list and care-as-usual controls) were responsible for 33.3% of the overall improvement, non-specific factors (the effects of NDST compared with control groups) for 49.6%, and specific factors (the effects of NDST compared with other therapies) for 17.1%. NDST has a considerable effect on symptoms of depression. Most of the effect of therapy for adult depression is realized by non-specific factors, and our results suggest that the contribution of specific effects is limited at best.

[Liver transplantation - when and for whom it should be performed]

During the past two decades, orthotopic liver transplantation (OLT) emerged to the treatment of choice for patients with end-stage liver disease. In Switzerland, about 100 liver transplantations are performed every year, while the shortage of cadaveric organs considerably outmatches the demand. Common indications for OLT include cirrhosis due to alcoholic liver disease or chronic viral hepatitis related to hepatitis B or C, and hepatocellular carcinoma. With the advent of the new allocation policy in Switzerland in 2007, patients listed for OLT are mainly stratified based on the Model of End-stage Liver Disease (MELD) score. Using a patient's laboratory values for serum bilirubin, serum creatinin, and the international normalized ratio for prothrombin time (INR), the MELD score accurately predicts three-month mortality among patients on the waiting list. Compared to the pre-MELD era, patients with significantly higher MELD scores undergo transplantation which leads in turn to more complications and higher costs yet with a comparable outcome. Timely referral of potential candidates to a transplant center is crucial since thorough evaluation to rule out contraindications such as uncontrolled infection, extrahepatic malignancy or advanced cardiopulmonary disease is essential. Taken together, every patient presenting with acute liver failure, decompensated cirrhosis or suspected hepatocellular carcinoma should be evaluated in a center with liver transplantation capability.

Organ donation in Switzerland: a survey on marginal or extended criteria donors (ECD) from 1998 to 2009

The widening gap between the numbers of patients on the waiting list for organ transplantation and the insufficient numbers of organ donors results in the use of "critical" donors, so-called marginal donors or extended criteria donors. Data concerning the evaluation of extended criteria donors (ECD) in Switzerland are sparse.

Taiji practice attenuates psychobiological stress reactivity - A randomized controlled trial in healthy subjects

Background: Stress reducing effects of Taiji, a mindful and gentle form of body movement, have been reported in previous studies, but standardized and controlled experimental studies are scarce. The present study investigates the effect of regular Taiji practice on psychobiological stress response in healthy men and women. Methods: 70 participants were randomly assigned to either Taiji classes or a waiting list. After 3 months, 26 (8 men, 18 women) persons in the Taiji group and 23 (9 men, 14 women) in the waiting control group underwent a standardized psychosocial stress test combining public speaking and mental arithmetic in front of an audience. Salivary cortisol and α-amylase, heart rate, and psychological responses to psychosocial stress were compared between the study groups. (ClinicalTrials.gov number, NCT01122706.) Results: Stress induced characteristic changes in all psychological and physiological measures. Compared to controls, Taiji participants exhibited a significantly lower stress reactivity of cortisol (p = .028) and heart rate (p = .028), as well as lower α-amylase levels (p = .049). They reported a lower increase in perceived stressfulness (p = .006) and maintained a higher level of calmness (p = .019) in response to psychosocial stress. Conclusion: Our results consistently suggest that practicing Taiji attenuates psychobiological stress reactivity in healthy subjects. This may underline the role of Taiji as a useful mind–body practice for stress prevention.

Continuous flow left ventricular assist devices: a valid option for heart failure patients

Recent outstanding clinical advances with new mechanical circulatory systems (MCS) have led to additional strategies in the treatment of end stage heart failure (HF). Heart transplantation (HTx) can be postponed and for certain patients even replaced by smaller implantable left ventricular assist devices (LVAD). Mechanical support of the failing left ventricle enables appropriate hemodynamic stabilisation and recovery of secondary organ failure, often seen in these severely ill patients. These new devices may be of great help to bridge patients until a suitable cardiac allograft is available but are also discussed as definitive treatment for patients who do not qualify for transplantation. Main indications for LVAD implantation are bridge to recovery, bridge to transplantation or destination therapy. LVAD may be an important tool for patients with an expected prolonged period on the waiting list, for instance those with blood group 0 or B, with a body weight over 90 kg and those with potentially reversible secondary organ failure and pulmonary artery hypertension. However, LVAD implantation means an additional heart operation with inherent peri-operative risks and complications during the waiting period. Finally, cardiac transplantation in patients with prior implantation of a LVAD represents a surgical challenge. This review summarises the current knowledge about LVAD and continuous flow devices especially since the latter have been increasingly used worldwide in the most recent years. The review is also based on the institutional experience at Berne University Hospital between 2000 and 2012. Apart from short-term devices (Impella, Cardiac Assist, Deltastream and ECMO) which were used in approximately 150 cases, 85 pulsatile long-term LVAD, RVAD or bi-VAD and 44 non-pulsatile LVAD (mainly HeartMateII and HeartWare) were implanted. After an initial learning curve, one-year mortality dropped to 10.4% in the last 58 patients.

Early reperfusion hemodynamics predict recovery in rat hearts: a potential approach towards evaluating cardiac grafts from non-heart-beating donors

Aims Cardiac grafts from non-heartbeating donors (NHBDs) could significantly increase organ availability and reduce waiting-list mortality. Reluctance to exploit hearts from NHBDs arises from obligatory delays in procurement leading to periods of warm ischemia and possible subsequent contractile dysfunction. Means for early prediction of graft suitability prior to transplantation are thus required for development of heart transplantation programs with NHBDs. Methods and Results Hearts (n = 31) isolated from male Wistar rats were perfused with modified Krebs-Henseleit buffer aerobically for 20 min, followed by global, no-flow ischemia (32°C) for 30, 50, 55 or 60 min. Reperfusion was unloaded for 20 min, and then loaded, in working-mode, for 40 min. Left ventricular (LV) pressure was monitored using a micro-tip pressure catheter introduced via the mitral valve. Several hemodynamic parameters measured during early, unloaded reperfusion correlated significantly with LV work after 60 min reperfusion (p<0.001). Coronary flow and the production of lactate and lactate dehydrogenase (LDH) also correlated significantly with outcomes after 60 min reperfusion (p<0.05). Based on early reperfusion hemodynamic measures, a composite, weighted predictive parameter, incorporating heart rate (HR), developed pressure (DP) and end-diastolic pressure, was generated and evaluated against the HR-DP product after 60 min of reperfusion. Effective discriminating ability for this novel parameter was observed for four HR*DP cut-off values, particularly for ≥20 *103 mmHg*beats*min−1 (p<0.01). Conclusion Upon reperfusion of a NHBD heart, early evaluation, at the time of organ procurement, of cardiac hemodynamic parameters, as well as easily accessible markers of metabolism and necrosis seem to accurately predict subsequent contractile recovery and could thus potentially be of use in guiding the decision of accepting the ischemic heart for transplantation.

Not in the Legends

In writing “Not in the Legends”, one of the images and concepts which constantly returned was that of pilgrimage. I began to write these poems while studying abroad in London, after having passed the previous semester in France and travelling around Europe. There was something in the repetition of sightseeing— walking six miles in Luxembourg to see the grave of General Patton, taking photographs of the apartment where Sylvia Plath ended her life, bowing before the bones of saints, searching through Père Lachaise for the grave of Théodore Gericault— which struck me as numinous and morbid. At the same time, I came to love living abroad and I grew discontent with both remaining and returning. I wanted the opportunity to live everywhere all the time and not have to choose between home and away. Returning from abroad, I turned my attention to the landscape of my native country. I found in the New England pilgrims a narrative of people who had left their home in search of growth and freedom. In these journeys I began to appreciate the significance of place and tried to understand what it meant to move from one place to another, how one chose a home, and why people searched for meaning in specific locations. The processes of moving from student to worker and from childhood to adulthood have weighed on me. I began to see these transitions towards maturity as travels to a different land. Memory and nostalgia are their own types of pilgrimage in their attempts to return to lost places, as is the reading of literature. These pilgrimages, real and metaphorical, form the thematic core of the collection. I read the work of many poets who came before me, returning to the places where the Canon was forged. Those poets have a large presence in the work I produced. I wondered how I, as a young poet, could earn my own place in the tradition and sought models in much the same way a painter studies the brushstrokes of a master. In the process, I have tried to uncover what it means to be a poet. Is it something like being a saint? Is it something like being a colonist? Or is to be the one who goes in search of saints and colonists? In trying to measure my own life and work based on the precedent, I have questioned what role era and generation have on the formation of identity. I focused my reading heavily on the early years of English poetry, trying to find the essence of the time when the language first achieved the transcendence of verse. In following the development of English poetry through Coleridge, John Berryman, and Allison Titus, I have explored the progression of those basic virtues in changing contexts. Those bearings, applied to my modern context, helped to shape the poetry I produced. Many of the poems in “Not in the Legends” are based on my own personal experience. In my recollections I have tried to interrogate nostalgia rather than falling into mere reminiscence. Rather than allowing myself poems of love and longing, I have tried to find the meaning of those emotions. A dominant conflict exists between adventure and comfort which mirrors the central engagement with the nature of being “here” or “there”. It is found in scenes of domesticity and wilderness as I attempt to understand my own simultaneous desire for both. For example, in “Canned Mangoes…” the intrusion of nature, even in a context as innocuous as a poem by Sir Walter Raleigh, unravels ordinary comforts of the domestic sphere. The character of “The Boy” from Samuel Beckett’s Waiting for Godot proved such an interesting subject for me because he is one who can transcend the normal boundaries of time and place. The title suggests connections to both place and time. “Legends” features the dual meaning of both myths and the keys to maps. To propose something “Not in the Legends” is to find something which has no precedent in our histories and our geographies, something beyond our field of knowledge and wholly new. One possible interpretation I devised was that each new generation lives a novel existence, the future being the true locus of that which is beyond our understanding. The title comes from Keats’ “Hyperion, a Fragment”, and details the aftermath of the Titanomachy. The Titans, having fallen to the Olympians, are a representation of the passing of one generation for the next. Their dejection is expressed by Saturn, who laments: Not in my own sad breast, Which is its own great judge and searcher out, Can I find reason why ye should be thus: Not in the legends of the first of days… (129-132) The emotions of the conquered Titans are unique and without antecedent. They are experiencing feelings which surpass all others in history. In this, they are the equivalent of the poet who feels that his or her own sufferings are special. In contrast are Whitman’s lines from “Song of Myself” which serve as an epigraph to this collection. He contends for a sense of continuity across time, a realization that youth, age, pleasure, and suffering have always existed and will always exist. Whitman finds consolation in this unity, accepting that kinship with past generations is more important that his own individuality. These opposing views offer two methods of presenting the self in history. The instinct of poetry suggests election. The poet writes because he feels his experiences are special, or because he believes he can serve as a synecdoche for everyone. I have fought this instinct by trying to contextualize myself in history. These poems serve as an attempt at prosopography with my own narrative a piece of the whole. Because the earth abides forever, our new stories get printed over the locations of the old and every place becomes a palimpsest of lives and acts. In this collection I have tried to untangle some of those layers, especially my own, to better understand the sprawling legend of history.

Health status and health care utilisation of patients in complementary and conventional primary care in Switzerland--an observational study

BACKGROUND: The study is part of a nationwide evaluation of complementary and alternative medicine (CAM) in primary care in Switzerland. OBJECTIVES: Patient health status with respect to demographic attributes such as gender, age, and health care utilisation pattern was studied and compared with conventional primary care. METHODS: The study was performed as a cross-sectional survey including 11932 adult patients seeking complementary or conventional primary care. Patients were asked to document their self-perceived health status by completing a questionnaire in the waiting room. Physicians were performing conventional medicine and/or various forms of complementary primary care such as homeopathy, anthroposophic medicine, neural therapy, herbal medicine, or traditional Chinese medicine. Additional information on patient demographics and yearly consultation rates for participating physicians was obtained from the data pool of all Swiss health insurers. These data were used to confirm the survey results. RESULTS: We observed considerable and significant differences in demographic attributes of patients seeking complementary and conventional care. Patients seeking complementary care documented longer lasting and more severe main health problems than patients in conventional care. The number of previous physician visits differed between patient groups, which indicates higher consumption of medical resources by CAM patients. CONCLUSIONS: The study supports the hypothesis of differences in socio-demographic and behavioural attributes of patients seeking conventional medicine or CAM in primary care. The study provides empirical evidence that CAM users are requiring more physician-based medical services in primary care than users of conventional medicine.

Bridging hyperacute liver failure by ABO-incompatible auxiliary partial orthotopic liver transplantation

Uncontrollable intracranial pressure elevation in hyperacute liver failure often proves fatal if no suitable liver for transplantation is found in due time. Both ABO-compatible and auxiliary partial orthotopic liver transplantation have been described to control such scenario. However, each method is associated with downsides in terms of immunobiology, organ availability and effects on the overall waiting list.

[Survival, clinical data and quality of life 10 years after heart transplantation: a prospective study]

AIM: To study prospectively patients after heart transplantation with respect to quality of life, mortality, morbidity, and clinical parameters before and up to 10 years after the operation. METHODS: Sixty patients (47.9 +/- 10.9 years, 57 men, 3 women) were transplanted at the University of Vienna Hospital, Department for Heart and Thorax Surgery and were included in this study. They were assessed when set on the waiting list, then exactly one, 5 and 10 years after the transplantation. The variables evaluated included physical and emotional complaints, well-being, mortality and morbidity. In the sample of patients who survived 10 years (n = 23), morbidity (infections, malignancies, graft arteriosclerosis, and rejection episodes) as well as quality of life were evaluated. RESULTS: Actuarial survival rates were 83.3, 66.7, 48.3% at 1, 5, and 10 years after transplantation, respectively. During the first year, infections were the most important reasons for premature death. As a cause of mortality, malignancies were found between years 1 and 5, and graft arteriosclerosis between years 5 and 10. Physical complaints diminished significantly after the operation, but grew significantly during the period from 5 to 10 years (p < 0.001). However, trembling (p < 0.05) and paraesthesies (p < 0.01) diminished continuously. Emotional complaints such as depression and dysphoria (both p < 0.05) increased until the tenth year after their nadir at year 1. In long-time survivors, 3 malignancies (lung, skin, thyroidea) were diagnosed 6 to 9 years postoperatively. Three patients (13%) had signs of graft arteriosclerosis at year 10; 9 (40%) patients suffered from rejection episodes during the course of 10 years. There were no serious rejection episodes deserving immediate therapy. Quality of life at 10 years is good in these patients. CONCLUSIONS: Heart transplantation is a successful therapy for patients with terminal heart disease. Long-term survivors feel well after 10 years and report a good quality of life.