Observation of tau neutrino appearance in the CNGS beam with the OPERA experiment

The OPERA experiment is searching for νμ → ντ oscillations in appearance mode, i.e., via the direct detection of τ leptons in ντ charged-current interactions. The evidence of νμ → ντ appearance has been previously reported with three ντ candidate events using a sub-sample of data from the 2008–2012 runs. We report here a fourth ντ candidate event, with the τ decaying into a hadron, found after adding the 2012 run events without any muon in the final state to the data sample. Given the number of analyzed events and the low background, νμ → ντ oscillations are established with a significance of 4.2σ.

Hairless Streaks in Cattle Implicate TSR2 in Early Hair Follicle Formation

Four related cows showed hairless streaks on various parts of the body with no correlation to the pigmentation pattern. The stripes occurred in a consistent pattern resembling the lines of Blaschko. The non-syndromic hairlessness phenotype observed occurred across three generations of a single family and was compatible with an X-linked mode of inheritance. Linkage analysis and subsequent whole genome sequencing of one affected female identified two perfectly associated non-synonymous sequence variants in the critical interval on bovine chromosome X. Both variants occurred in complete linkage disequilibrium and were absent in more than 3900 controls. An ERCC6L missense mutation was predicted to cause an amino acid substitution of a non-conserved residue. Analysis in mice showed no specific Ercc6l expression pattern related to hair follicle development and therefore ERCC6L was not considered as causative gene. A point mutation at the 5'-splice junction of exon 5 of the TSR2, 20S rRNA accumulation, homolog (S. cerevisiae), gene led to the production of two mutant transcripts, both of which contain a frameshift and generate a premature stop codon predicted to truncate approximately 25% of the protein. Interestingly, in addition to the presence of both physiological TSR2 transcripts, the two mutant transcripts were predominantly detected in the hairless skin of the affected cows. Immunohistochemistry, using an antibody against the N-terminal part of the bovine protein demonstrated the specific expression of the TSR2 protein in the skin and the hair of the affected and the control cows as well as in bovine fetal skin and hair. The RNA hybridization in situ showed that Tsr2 was expressed in pre- and post-natal phases of hair follicle development in mice. Mammalian TSR2 proteins are highly conserved and are known to be broadly expressed, but their precise in vivo functions are poorly understood. Thus, by dissecting a naturally occurring mutation in a domestic animal species, we identified TSR2 as a regulator of hair follicle development.

Characterization of the Capacitance of a Rotating Ring–Disk Electrode

The use of rotating ring–disk electrodes as generator-collector systems has so far been limited to the detection of Faradaic currents at the ring. As opposed to other generator-collector configurations, non-Faradaic detection has not yet been carried out with rotating ring–disk electrodes. In this study, a.c. perturbation based detection for measurement of the ring impedance is introduced. By using a conducting polymer-modified disk electrode in combination with a bare gold ring as a model, it is shown that the measured ring capacitance correlates with the polarization of the polymer film, most probably due to counter-ion exchange. A method of calculating the ring capacitance based on a small-signal sinusoid perturbation is described and the most important instrumental limitations are identified.

Ventilation/perfusion SPECT or SPECT/CT for lung function imaging in patients with pulmonary emphysema?

PURPOSE To evaluate the utility of attenuation correction (AC) of V/P SPECT images for patients with pulmonary emphysema. MATERIALS AND METHODS Twenty-one patients (mean age 67.6 years) with pulmonary emphysema who underwent V/P SPECT/CT were included. AC/non-AC V/P SPECT images were compared visually and semiquantitatively. Visual comparison of AC/non-AC images was based on a 5-point likert scale. Semiquantitative comparison assessed absolute counts per lung (aCpLu) and lung lobe (aCpLo) for AC/non-AC images using software-based analysis; percentage counts (PC = (aCpLo/aCpLu) × 100) were calculated. Correlation between AC/non-AC V/P SPECT images was analyzed using Spearman's rho correlation coefficient; differences were tested for significance with the Wilcoxon rank sum test. RESULTS Visual analysis revealed high conformity for AC and non-AC V/P SPECT images. Semiquantitative analysis of PC in AC/non-AC images had an excellent correlation and showed no significant differences in perfusion (ρ = 0.986) or ventilation (ρ = 0.979, p = 0.809) SPECT/CT images. CONCLUSION AC of V/P SPECT images for lung lobe-based function imaging in patients with pulmonary emphysema do not improve visual or semiquantitative image analysis.

Lexical Pragmatics and Theory of Mind: The Acquisition of Connectives

The concept of theory of mind (ToM), a hot topic in cognitive psychology for the past twenty-five years, has gained increasing importance in the fields of linguistics and pragmatics. However, even though the relationship between ToM and verbal communication is now recognized, the extent, causality and full implications of this connection remain mostly to be explored. This book presents a comprehensive discussion of the interface between language, communication, and theory of mind, and puts forward an innovative proposal regarding the role of discourse connectives for this interface. The proposed analysis of connectives is tested from the perspective of their acquisition, using empirical methods such as corpus analysis and controlled experiments, thus placing the study of connectives within the emerging framework of experimental pragmatics.

Evaluation of epidemiological and clinical factors in survival of patients with de novo myelodysplastic syndrome at the University of Texas MD Anderson cancer center

Little is known about epidemiological markers that are associated with survival of patients with myelodysplastic syndromes (MDS). We conducted a secondary case-based analysis of 465 de novo MDS patients from the University of Texas MD Anderson Cancer Center (UTMDACC). We investigated the association between demographic as well as occupational exposure markers and survival while incorporating known clinical markers of prognosis. In our patient population, 60.6% were men and the majority were white (93.1%). The distribution of MDS subtypes by the French–American–British (FAB) classification was 81 (19%) refractory anemia (RA), 46 (9.9%) refractory anemia with ringed sideroblasts (RARS), 57 (12.3%) chronic myelomonocytic leukemia (CMML), 173 (37.2%) RA with excess blasts (RAEB), and 86 (18.5%) RAEB in transformation (RAEBT). We found that those older at diagnosis (> 60 years of age) (HR = 1.68, CI = 1.26-2.25) were at a higher risk of dying compared to younger patients. Similarly, high pack years of smoking (>= 30 pack years of smoking) (HR = 1.34, CI = 1.02-1.74), and agricultural chemical exposure (HR = 1.61, CI = 1.05-2.46) were significantly associated with overall lower survival when compared to patients with none or medium exposures. Among clinical markers, greater than 5% bone marrow blasts (HR = 1.81 CI = 1.27-2.56), poor cytogenetics (HR = 3.20, CI = 2.37-4.33)), and platelet cytopenias (<100000/ul) (HR = 1.46, CI = 1.11-1.92) were also significantly associated with overall MDS survival.^ The identification of epidemiological markers could help physicians stratify patients and customize treatment strategies to improve the outcome of MDS based on patient lifestyle information such as smoking exposure and agrochemical exposure. We hope that this study highlights the impact of these exposures in MDS prognosis.^

Systems Biology Approaches to Probe Gene Regulation in Bacteria

Mechanisms that allow pathogens to colonize the host are not the product of isolated genes, but instead emerge from the concerted operation of regulatory networks. Therefore, identifying components and the systemic behavior of networks is necessary to a better understanding of gene regulation and pathogenesis. To this end, I have developed systems biology approaches to study transcriptional and post-transcriptional gene regulation in bacteria, with an emphasis in the human pathogen Mycobacterium tuberculosis (Mtb). First, I developed a network response method to identify parts of the Mtb global transcriptional regulatory network utilized by the pathogen to counteract phagosomal stresses and survive within resting macrophages. As a result, the method unveiled transcriptional regulators and associated regulons utilized by Mtb to establish a successful infection of macrophages throughout the first 14 days of infection. Additionally, this network-based analysis identified the production of Fe-S proteins coupled to lipid metabolism through the alkane hydroxylase complex as a possible strategy employed by Mtb to survive in the host. Second, I developed a network inference method to infer the small non-coding RNA (sRNA) regulatory network in Mtb. The method identifies sRNA-mRNA interactions by integrating a priori knowledge of possible binding sites with structure-driven identification of binding sites. The reconstructed network was useful to predict functional roles for the multitude of sRNAs recently discovered in the pathogen, being that several sRNAs were postulated to be involved in virulence-related processes. Finally, I applied a combined experimental and computational approach to study post-transcriptional repression mediated by small non-coding RNAs in bacteria. Specifically, a probabilistic ranking methodology termed rank-conciliation was developed to infer sRNA-mRNA interactions based on multiple types of data. The method was shown to improve target prediction in Escherichia coli, and therefore is useful to prioritize candidate targets for experimental validation.

Exploration of genetic susceptibility to pancreatic cancer: A GWAS approach

Pancreatic cancer is the 4th most common cause for cancer death in the United States, accompanied by less than 5% five-year survival rate based on current treatments, particularly because it is usually detected at a late stage. Identifying a high-risk population to launch an effective preventive strategy and intervention to control this highly lethal disease is desperately needed. The genetic etiology of pancreatic cancer has not been well profiled. We hypothesized that unidentified genetic variants by previous genome-wide association study (GWAS) for pancreatic cancer, due to stringent statistical threshold or missing interaction analysis, may be unveiled using alternative approaches. To achieve this aim, we explored genetic susceptibility to pancreatic cancer in terms of marginal associations of pathway and genes, as well as their interactions with risk factors. We conducted pathway- and gene-based analysis using GWAS data from 3141 pancreatic cancer patients and 3367 controls with European ancestry. Using the gene set ridge regression in association studies (GRASS) method, we analyzed 197 pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Using the logistic kernel machine (LKM) test, we analyzed 17906 genes defined by University of California Santa Cruz (UCSC) database. Using the likelihood ratio test (LRT) in a logistic regression model, we analyzed 177 pathways and 17906 genes for interactions with risk factors in 2028 pancreatic cancer patients and 2109 controls with European ancestry. After adjusting for multiple comparisons, six pathways were marginally associated with risk of pancreatic cancer ( P < 0.00025): Fc epsilon RI signaling, maturity onset diabetes of the young, neuroactive ligand-receptor interaction, long-term depression (Ps < 0.0002), and the olfactory transduction and vascular smooth muscle contraction pathways (P = 0.0002; Nine genes were marginally associated with pancreatic cancer risk (P < 2.62 × 10−5), including five reported genes (ABO, HNF1A, CLPTM1L, SHH and MYC), as well as four novel genes (OR13C4, OR 13C3, KCNA6 and HNF4 G); three pathways significantly interacted with risk factors on modifying the risk of pancreatic cancer (P < 2.82 × 10−4): chemokine signaling pathway with obesity ( P < 1.43 × 10−4), calcium signaling pathway (P < 2.27 × 10−4) and MAPK signaling pathway with diabetes (P < 2.77 × 10−4). However, none of the 17906 genes tested for interactions survived the multiple comparisons corrections. In summary, our current GWAS study unveiled unidentified genetic susceptibility to pancreatic cancer using alternative methods. These novel findings provide new perspectives on genetic susceptibility to and molecular mechanisms of pancreatic cancer, once confirmed, will shed promising light on the prevention and treatment of this disease. ^

Strange bedfellows: The ethics and politics of medical futility in Texas

Background: Futile medical treatments are interventions that are not associated with a benefit to the patient. The definition and concept of medical futility are controversial. The Texas Advance Directives Act (TADA) was passed in 1999 to address medically inappropriate interventions by allowing providers to withdraw inappropriate interventions against a surrogate decision maker's wishes following a review, attempt to transfer the patient, and 10-day waiting period. The original legislation was a negotiated compromise by players across the political spectrum. However, in recent years there has been increasing controversy regarding TADA and attempts to alter its applicability in Texas. ^ Purpose: The purpose of this project was to apply Paul Sabatier's advocacy coalition framework (ACF) to gain understanding into the historical, ethical, and political basis of the initial compromise, and determine the sources of conflict that have led to increased opposition to TADA. ^ Methods: Using the ACF model, key actors within the medical futility policy debate in Texas were aggregated into coalitions based on shared beliefs. A narrative summary based analysis identified the core elements of the policy subsystem, as well as the constraints and resources of the subsystem actors. Externalities that promoted adjustments to coalition beliefs and tactics used by coalition participants were analyzed. Data sources included review of the published literature regarding medical futility, as well as analysis of published newspaper accounts and editorials regarding the medical futility issue in Texas, legislative testimony, and review of weblogs and online commentaries dealing with the issue. ^ Results: Primary coalition participants in developing compromise legislation in 1999 were the Providers and Vitalists, with Autonomists gaining a prominent role starting in 2006. Internal factors associated with the breakdown of consensus included changes to the makeup of the governing coalition and changes in individual case information available to the Vitalist coalition. Externalities related to the intertwining of the Sun Hudson case and the Terri Schiavo case generated negative publicity for the TADA from progressive and conservative viewpoints. Dissemination of information in various venues regarding contentious cases was associated with more polarization of viewpoints, and realignment of coalition alliances. ^ Conclusions: The ACF provided an outline for the initial compromise over the creation of the Texas Advance Directives Act as well as the eventual loss of consensus. The debate between the Provider, Vitalist, and Autonomist coalitions has been affected by internal policy evolution, changes in the governing coalition, and important externalities. The debate over medical futility in Texas has had much broader implications in the dispute over Health Care Reform.^

Obtención de un estándar secundario de cuantificación para la síntesis y purificación de allicina.

Desde tiempos ancestrales, el ajo (Allium sativum L.) ha sido utilizado para la prevención y el tratamiento de dolencias. Sus efectos benéficos para la salud han sido atribuidos a los tiosulfinatos, siendo la allicina el más abundante. La determinación rutinaria de la allicina es dificultosa dada su inestabilidad y la naturaleza reactiva de la misma. El objetivo del trabajo fue obtener un estándar secundario para la cuantificación de allicina mediante Cromatografía Líquida de Alta Resolución (HPLC). Fueron ensayadas diferentes metodologías de síntesis y purificación de allicina. En el Laboratorio de Residuos Tóxicos de la Fac. Cs. Agrarias (UNCuyo), bajo condiciones controladas, se preparó polvo de ajo para ser utilizado como estándar secundario de cuantificación. La cuantificación de muestras problema contra ambos estándares (allicina pura y polvo de ajo estandarizado, respectivamente) no presentó diferencias significativas. El empleo de polvo de ajo estandarizado ofrece una alternativa viable simple para la cuantificación de allicina.

Interstitial water d13C and sediment geochemistry of ODP Leg 166 sites

A review of interstitial water samples collected from Sites 1003-1007 of the Bahamas Transect along with a shore-based analysis of oxygen and carbon isotopes, minor and trace elements, and sediment chemistry are presented. Results indicate that the pore-fluid profiles in the upper 100 meters below seafloor (mbsf) are marked by shifts between 20 and 40 mbsf that are thought to be caused by changes in sediment reactivity, sedimentation rates, and the influence of strong bottom currents that have been active since the late Pliocene. Pore-fluid profiles in the lower Pliocene-Miocene sequences are dominated by diffusion and do not show significant evidence of subsurface advective flow. Deeper interstitial waters are believed to be the in situ fluids that have evolved through interaction with sediments and diffusion. Pore-fluid chemistry is strongly influenced by carbonate recrystallization processes. Increases in pore-fluid Cl- and Na+ with depth are interpreted to result mainly from carbonate remineralization reactions that are most active near the platform margin. A lateral gradient in detrital clay content observed along the transect, leads to an overall lower carbonate reactivity, and enhances preservation of metastable aragonite further away from the platform margin. Later stage burial diagenesis occurs at slow rates and is limited by the supply of reactive elements through diffusion.

Age models and sea-surface paleotemperature reconstruction of sediment cores from the eastern equatorial Atlantic

Based on the faunal record of planktonic foraminifers in three long gravity sediment cores from the eastern equatorial Atlantic, the sea-surface temperature history ove the last 750,000 years was studied at a resolution of 3,000 to 10,000 years. Detailed oxygen-isotope and paleomagnetic stratigraphy helped to identify the following major faunal events: Globorotaloides hexagonus and Globorotalia tumida flexuosa became extinct in the eastern tropical Atlantic at the isotope stage 4/5 boundary, now dated at 68,000 years B.P. The persistent occurrence of the pink variety of Globigerinoides ruber started during the late stage 12 at 410,000 years B.P. CARTUNE-age. This datum may provide an easily detectible faunal stratigraphic marker for the mid-Brunhes Chron. The updated scheme of the Ericson zones helped the recognition of a hiatus at the northwestern slope of the Sierra Leone Basin covering oxygen-isotope stages 10 to 12. Classifying the planktonic foraminifer counts into six faunal assemblages, according to the factor analysis derived model of Pflaumann (1985), the tropical and the tropical-upwelling communities account for 57 % at Site 16415, and 86 % at Site 13519, respectively of the variance of the faunal record. A largely continuous paleotemperature record for both winter and summer seasons was obtained from the top of the Sierra Leone Rise with the winter temperatures ranging between 20 and 25 °C, and the summer ones between 24 and 30 °C. The record of cores from greater water depths is frequently interrupted by samples with no-analogue faunal communities and/or poor preservation. Based on the seasonality signal, during cold periods the termal equator shifted to a geographically mnore asymmetrical northern position. Dissolution altering the faunal communities becomes stronger with greater water depth, the estimated mean minimum loss of specimens increases from 70 % to 80 % between 2,860 and 3,850 water depth although some species will be more susceptible than others. Enhanced dissolution occured during stage 4 but also during cold phases in the warm stage 7 and 9. Correlations between the Foraminiferal Dissolution Index and the estimated sea-surface temperatures are significant. Foraminiferal flux rates, negatively correlated to the flux rates of organic carbon and of diatoms, may be a result of enhanced dissolution during cold stages, destroying still more of the faunal signal than indicated by the calculated minimum loss. The fluctuations of the oxygen-isotope curves and the hibernal sea-surfave temperatures are fairly coherent. During warm oxygen-isotope stages the temperature maxima lag often by 5 to 15 ka behind the respective sotope minima. During cold stages, sea-surface temperature changes are partly out of phase and contain additional fluctuations.

On-board and Ground Visual Pose Estimation Techniques for UAV Control

In this paper, two techniques to control UAVs (Unmanned Aerial Vehicles), based on visual information are presented. The first one is based on the detection and tracking of planar structures from an on-board camera, while the second one is based on the detection and 3D reconstruction of the position of the UAV based on an external camera system. Both strategies are tested with a VTOL (Vertical take-off and landing) UAV, and results show good behavior of the visual systems (precision in the estimation and frame rate) when estimating the helicopter¿s position and using the extracted information to control the UAV.

Abstraction carrying code and resource-awareness

Proof-Carrying Code (PCC) is a general approach to mobile code safety in which the code supplier augments the program with a certifícate (or proof). The intended benefit is that the program consumer can locally validate the certifícate w.r.t. the "untrusted" program by means of a certifícate checker—a process which should be much simpler, eíñcient, and automatic than generating the original proof. Abstraction Carrying Code (ACC) is an enabling technology for PCC in which an abstract model of the program plays the role of certifícate. The generation of the certifícate, Le., the abstraction, is automatically carried out by an abstract interpretation-based analysis engine, which is parametric w.r.t. different abstract domains. While the analyzer on the producer side typically has to compute a semantic fixpoint in a complex, iterative process, on the receiver it is only necessary to check that the certifícate is indeed a fixpoint of the abstract semantics equations representing the program. This is done in a single pass in a much more efficient process. ACC addresses the fundamental issues in PCC and opens the door to the applicability of the large body of frameworks and domains based on abstract interpretation as enabling technology for PCC. We present an overview of ACC and we describe in a tutorial fashion an application to the problem of resource-aware security in mobile code. Essentially the information computed by a cost analyzer is used to genérate cost certificates which attest a safe and efficient use of a mobile code. A receiving side can then reject code which brings cost certificates (which it cannot validate or) which have too large cost requirements in terms of computing resources (in time and/or space) and accept mobile code which meets the established requirements.

Non-destructive measurements of the optical properties of apples by means of time-resolved reflectance

Time-resolved reflectance is proposed and effectively used for the nondestructive measurement of the optical properties in apples. The technique is based on the detection of the temporal dispersion of a short laser pulse injected into the probed medium. The time-distribution of re-emitted photons interpreted with a solution of the Diffusion equation yields the mean values of the absorption and reduced scattering coefficients of the medium. The proposed technique proved valuable for the measurement of the absorption and scattering spectra of different varieties of apples. No major variations were observed in the experimental data when the fruit was peeled, proving that the measured optical properties are referred to the pulp. The depth of probed volume was determined to be about 2 cm. Finally, the technique proved capable to follow the change in chlorophyll absorption during storage.