Sedimen-water nutrient fluxes: Preliminary results of in situ measurements in Alfaques Bay, Ebro River Delta.

Sediment-water exchanges of oxygen, ammonium, nitrate, total dissolved nitrogen, phosphate and total dissolved phosphorus were measured by means of an in situ incubator of 7 1 volume and 700 cm2 base area. The incubations lasted for three hours and were done over a whole season on different kinds of sediments in Alfaques Bay. We present some preliminary results on: i) methodological aspects, ii) spatial and temporal variability of fluxes, and iii) estimates of contribution of benthic nutrient regeneration relative to total nutrient loading of the Bay. Oxygen uptake averaged 1700 mmo1 m-2 h-1 (range 200-3500); no differences were found between sandy and muddy sediments. The release of ammonia from the sediment averaged 70 mmo1 m-2 h-1 and was higher in muddy sediments than in sandy ones. Very low to null nitrate and nitrite fluxes and only small fluxes of organic nitrogen were detected. We conclude that ammonium release from sediment is the major path of nitrogen regeneration. Some sediments removed dissolved reactive phosphorus (DRP) from the water and released dissolved organic phosphorus (DOP). Additional manipulative experiments revealed DRP release under particular conditions (turbulence, anoxia). From these data, we estimate that at least 50% of the nitrogen requirements of phytoplankton in the area may be supplied by benthic remineralization.

Determinação de capacidade de campo in situ ou através de equações de regressão

Este trabalho foi desenvolvido com os objetivos de testar as equações globais obtidas por Macedo para determinar a capacidade de campo (CC) in situ em um solo Podzólico Vermelho-Amarelo; avaliar a câmara de fluxo desenvolvida por Fabian & Ottoni Filho; e verificar se os valores de CC obtidos com esse equipamento se comparam aos determinados pelo método da Embrapa. Os testes foram realizados em 1994, num Podzólico Vermelho-Amarelo, em Itaguaí, RJ. A motivação desta comparação é o fato de o movimento lateral da água ser praticamente eliminado dentro da câmara. Confirmou-se que os valores medidos de CC em tal equipamento reproduziram as determinações de CC obtidas pelo método da Embrapa. Como a área da câmara é de 0,50 m², o resultado sugere a possibilidade de reduzir a dimensão dos tabuleiros de inundação. Foram também validadas as equações globais de regressão para determinar a CC a partir de porcentagens texturais e de matéria orgânica, ou a partir da microporosidade (umidade a 60 cm de tensão).

The frequency and prognostic impact of dic(9;20)(p13.2;q11.2) in childhood B-cell precursor acute lymphoblastic leukemia: results from the NOPHO ALL-2000 trial.

The dic(9;20)(p13.2;q11.2) is reported to be present in ∼2% of childhood B-cell precursor acute lymphoblastic leukemia (BCP ALL). However, it easily escapes detection by G-banding analysis and its true prevalence is hence unknown. We performed interphase fluorescence in situ hybridization analyses-in a three-step manner-using probes for: (i) CDKN2A at 9p21, (ii) 20p and 20q subtelomeres and (iii) cen9 and cen20. Out of 1033 BCP ALLs diagnosed from 2001 to 2006, 533 were analyzed; 16% (84/533) displayed 9p21 deletions, of which 30% (25/84) had dic(9;20). Thus, dic(9;20)-positivity was found in 4.7% (25/533), making it the third most common genetic subgroup after high hyperdiploidy and t(12;21)(p13;q22). The dic(9;20) was associated with a female predominance and an age peak at 3 years; 18/25 (72%) were allocated to non-standard risk treatment at diagnosis. Including cases detected by G-banding alone, 29 dic(9;20)-positive cases were treated according to the NOPHO ALL 2000 protocol. Relapses occurred in 24% (7/29) resulting in a 5-year event-free survival of 0.69, which was significantly worse than for t(12;21) (0.87; P=0.002) and high hyperdiploidy (0.82; P=0.04). We conclude that dic(9;20) is twice as common as previously surmised, with many cases going undetected by G-banding analysis, and that dic(9;20) should be considered a non-standard risk abnormality.

Diagnostic and identification in situ of fungal pathogens in superficial mycosis

Fungi are divided in 3 groups in the field of medical mycology. The dermatophytes are filamentous fungi able to grow on keratinized tissues from human or animals. They are the main cause of superficial and cutaneous mycoses of the skin and its appendix (hair and nail). The yeasts, or dimorphic fungi, can be responsible of diverse types of infections (superficial to deep mycoses). The moulds include all Non-dermatophyte Filamentous Fungi (NDF). In medical mycology, the most representative moulds are Aspergillus spp., Fusarium spp. and Mucor spp. Diagnosis of mycosis is currently based on direct mycological examination of biological samples, as well as macroscopic and microscopic identification of the infectious fungus in culture assay. However, culture assays were found to remain sterile in roughly 40% of cases otherwise positive by direct mycological examinations. Additionally, results from culture assays are often difficult to interpret as various NDF are sometimes isolated. This thesis work is composed of three projects focusing on the development of new assays for direct in situ identification of fungi from dermatological samples. Part 1. A Polymerase Chain Reaction - Terminal Restriction Fragment Length Polymorphism assay (PCR-TRFLP) targeting the 28S rDNA was developed to identify dermatophytes and NDF in nails with suspected onychomycosis. This method is faster and more efficient than culture. It further enables the distinction of more than one agent in case of mixed infection. A fast and reliable assay for the identification of dermatophytes and NDF in onychomycosis was found to be highly relevant since onychomycosis with Fusarium spp. or other NDF are weakly responsive or unresponsive to standard onychomycosis treatments with oral terbinafine and itraconazole. Part 2. A nested PCR-sequencing assay targeting the 28S rDNA was developed to identify dermatophyte species in skin and hair samples. This method is especially suitable for tinea capitis where dermatophytes identification is critical for subsequently prescribing the adequate treatment. The challenge presented when performing direct PCR fungi identification in skin and hair differs from that seen in onychomycosis as small amount of material is generally collected, few fungal elements are present in the clinical sample and one dermatophyte among a dozen species must be identified. Part 3. Fusarium spp. is currently isolated from nails with a frequency of 15% of that of dermatophytes in the laboratory of Mycology of the CHUV (2005-2012). The aim of this work was to examine if the intensive use of terbinafine and itraconazole could be a cause of the high incidence of Fusarium nail infections. For that purpose, two different methods, specific PCR and TRFLP, were used to detect both Fusarium spp. and Trichophyton spp. in nails of previously treated or untreated patients. TRFLP assay was found to be less sensitive than classical PCR assays specifically detecting Fusarium spp. or Trichophyton spp. Independently of the detection method used, the prevalence of Fusarium spp. appears not to be higher in patients previously treated by oral standard treatment with terbinafine and azoles which are highly effective to fight Trichophyton spp. in nails. In many cases Fusarium sp. was detected in samples of patients not previously subjected to antifungal therapy. Therefore, these treatments do not appear to favor the establishment of Fusarium spp. after elimination of a dermatophyte in nail infection. - En mycologie médicale, les champignons sont classés en 3 groupes. Les dermatophytes sont des champignons filamenteux capables de se développer dans les tissus kératinisés des hommes et des animaux, ils représentent la principale cause des mycoses superficielles et cutanées de la peau et de ses appendices (ongles et cheveux). Les levures, ou champignons dimorphiques, peuvent être responsables de divers types d'infections (superficielles à profondes). Les moisissures incluent tous les champignons filamenteux non-dermatophytes (NDF), les Aspergillus spp., les Fusarium spp. et les Mucor spp. sont les principales espèces rencontrées. Le diagnostic d'une mycose est basé sur un examen mycologique direct des prélèvements biologiques ainsi que sur l'identification macroscopique et microscopique du champignon infectieux isolé en culture. Cependant, dans environ 40% des cas, l'identification de l'agent pathogène est impossible par cette méthode car la culture reste stérile, bien que l'examen direct soit positif. De plus, la croissance de moisissures et/ou autres contaminants peut rendre l'interprétation de l'examen difficile. Ce travail de thèse est composé de trois projets focalisés sur le développement de nouvelles méthodes d'identification des champignons directement à partir d'échantillons dermatologiques. Projet 1. Une méthode de Réaction en chaîne de polymérase couplée à du polymorphisme de longueur des fragments de restriction terminaux (PCR-TRFLP), en ciblant l'ADN ribosomal 28S, a été développée pour l'identification des dermatophytes et moisissures dans les ongles avec suspicion d'onychomycoses. Cette technique s'est avérée plus rapide et plus efficace que la culture, permettant l'identification de plusieurs champignons en même temps. Posséder une méthode d'identification rapide et fiable des dermatophytes et des NDF dans les onychomycoses a été jugée nécessaire du fait que les Fusarium et d'autres NDF sont peu ou pas sensibles aux traitements oraux standards à la terbinafine et à Γ itraconazole. Projet 2. Une PCR nichée couplée au séquençage d'un fragment de l'ADN ribosomal 28S a été développée afin de différencier les dermatophytes dans la peau et les cheveux. Cette méthode est particulièrement adaptée au cas de tinea capitis, où l'identification du dermatophyte est essentielle afin de prescrire le traitement adéquat. Le problème de l'identification du pathogène fongique dans les cheveux et la peau diffère des onychomycoses car de petites quantités sont prélevées chez les patients, peu d'éléments fongiques sont présents et il faut discriminer un dermatophyte parmi une douzaine d'espèces potentielles. Projet 3. Au laboratoire de Mycologie du CHUV, les Fusarium ont été isolé dans les ongles à une fréquence de 15% pour la période 2005-2012. Le but de ce travail était d'examiner si l'utilisation intensive de terbinafine et d'itraconazole pouvait être une des causes de la forte incidence des infections des ongles par Fusarium. A cet effet, deux méthodes ont été utilisées pour détecter à la fois Fusarium spp. et Trichophyton spp., la PCR spécifique et le TRFLP. Indépendamment de la méthode choisie, il en résulte que la prévalence des Fusarium η'apparaît pas liée à un traitement au préalable des patients avec de la terbinafine ou des azoles, thérapies très efficaces contre les Trichophyton spp. dans les ongles. De plus, il existe de nombreux cas où Fusarium était détecté chez des patients non traités.

In situ aortobiiliac reconstruction of infected aneurysm using a single superficial femoral vein.

Objective: To demonstrate successful in situ aortoiliac reconstruction of an infected infrarenal aneurysm using one single superficial femoral vein (SFV). Methods: In situ reconstruction using the right SFV sutured in end-to-end anastomosis with the aorta and distally with the right common iliac artery and in end-to-side anastomosis with the left common iliac artery. Results: The operating time was less than reported for aortic in situ reconstruction with bilateral SFV harvesting. The duplex scan 3 months postoperatively showed permeability of the bypass without any anastomotic stenosis or pseudoaneurysm. The right common femoral, popliteal, and greater saphenous veins were patent without thrombus, and the patient did not complain about peripheral edema. Conclusions: The use of only one instead of both the SFVs for aortobiiliac in situ reconstruction might be a way to reduce operating time and allow autogenous venous reconstruction even in patients with limited availability of venous material.

Degradabilidade in situ da matéria seca, da proteína bruta e da fibra de alguns alimentos

O objetivo deste trabalho foi determinar os parâmetros cinéticos da degradação, in situ, da matéria seca, da proteína bruta e da fibra em detergente neutro das silagens de milho e de capim-elefante, do feno de capim-Tifton 85 e do farelo de soja. Foram utilizados três bovinos adultos, fistulados no rúmen, com peso vivo médio de 400 kg. Os alimentos foram pesados em sacos de náilon, incubados todos de uma vez e retirados nos tempos 0, 2, 4, 8, 16, 24, 48 e 72 horas, após a incubação dos volumosos, e 0, 2, 4, 8, 16, 24 e 48 horas, após incubação do farelo de soja. Os resíduos dos sacos foram analisados quanto ao conteúdo de matéria seca, proteína bruta e fibra em detergente neutro. A matéria seca e a proteína bruta do farelo de soja apresentaram potencial de degradação elevado, assim como a proteína bruta da silagem de milho. Destacou-se a elevada fração não-degradável da fibra em detergente neutro do feno de capim-Tifton 85 e, portanto, sua baixa degradabilidade potencial da matéria seca. O teor de fibra em detergente neutro e suas características cinéticas exercem acentuado efeito sobre a digestão dos alimentos.

Genetic abnormalities and survival in multiple myeloma: the experience of the Intergroupe Francophone du Myélome.

Acquired genomic aberrations have been shown to significantly impact survival in several hematologic malignancies. We analyzed the prognostic value of the most frequent chromosomal changes in a large series of patients with newly diagnosed symptomatic myeloma prospectively enrolled in homogeneous therapeutic trials. All the 1064 patients enrolled in the IFM99 trials conducted by the Intergroupe Francophone du Myélome benefited from an interphase fluorescence in situ hybridization analysis performed on purified bone marrow plasma cells. They were systematically screened for the following genomic aberrations: del(13), t(11;14), t(4;14), hyperdiploidy, MYC translocations, and del(17p). Chromosomal changes were observed in 90% of the patients. The del(13), t(11;14), t(4;14), hyperdiploidy, MYC translocations, and del(17p) were present in 48%, 21%, 14%, 39%, 13%, and 11% of the patients, respectively. After a median follow-up of 41 months, univariate statistical analyses revealed that del(13), t(4;14), nonhyperdiploidy, and del(17p) negatively impacted both the event-free survival and the overall survival, whereas t(11;14) and MYC translocations did not influence the prognosis. Multivariate analyses on 513 patients annotated for all the parameters showed that only t(4;14) and del(17p) retained prognostic value for both the event-free and overall survivals. When compared with the currently used International Staging System, this prognostic model compares favorably. In myeloma, the genomic aberrations t(4;14) and del(17p), together with beta2-microglobulin level, are important independent predictors of survival. These findings have implications for the design of risk-adapted treatment strategies.

Digestibilidad in situ de dietas con harina de nopal deshidratado conteniendo un preparado de enzimas fibrolíticas exógenas

Se evaluó el efecto de un preparado de enzimas fibrolíticas exógenas (celulasas y xilanasas) en la degradabilidad in situ de la materia seca (DisMS), fibra detergente neutro (DFDNr) y fibra detergente ácido residual (DFDAr), en dietas altas o bajas en harina de nopal deshidratado. Se aplicaron concentraciones de 0, 1, 2 y 3 g de enzima por kilogramo de materia seca al inicio y 24 horas antes de la degradación in situ. Se determinó la concentración de ácidos grasos volátiles totales y de nitrógeno amoniacal a las 0, 3, 6, 9, 12 y 24 horas después de aplicarse la enzima. No se observaron efectos en DisMS, DFDNr y DFDAr; la aplicación al inicio de la degradación in situ mostró valores más altos que a 24 horas para DisMS y DFDNr, pero fue menor para DFDAr. No se observaron diferencias en las interacciones entre niveles de enzima, tipo de dieta y tiempo de pretratamiento. La aplicación de 1 y 3 g de enzima, en la dieta con bajo contenido de harina de nopal, tuvo efectos en el incremento de los ácidos grasos volátiles totales; para el nitrógeno amoniacal, los mejores resultados ocurrieron con 0 y 1 g de enzima.

Development of In Situ Detection Methods for Materials-Related Distress (MRD) in Concrete Pavements: Phase 2, HR-1081, 2005

This project utilized information from ground penetrating radar (GPR) and visual inspection via the pavement profile scanner (PPS) in proof-of-concept trials. GPR tests were carried out on a variety of portland cement concrete pavements and laboratory concrete specimens. Results indicated that the higher frequency GPR antennas were capable of detecting subsurface distress in two of the three pavement sites investigated. However, the GPR systems failed to detect distress in one pavement site that exhibited extensive cracking. Laboratory experiments indicated that moisture conditions in the cracked pavement probably explain the failure. Accurate surveys need to account for moisture in the pavement slab. Importantly, however, once the pavement site exhibits severe surface cracking, there is little need for GPR, which is primarily used to detect distress that is not observed visually. Two visual inspections were also conducted for this study by personnel from Mandli Communications, Inc., and the Iowa Department of Transportation (DOT). The surveys were conducted using an Iowa DOT video log van that Mandli had fitted with additional equipment. The first survey was an extended demonstration of the PPS system. The second survey utilized the PPS with a downward imaging system that provided high-resolution pavement images. Experimental difficulties occurred during both studies; however, enough information was extracted to consider both surveys successful in identifying pavement surface distress. The results obtained from both GPR testing and visual inspections were helpful in identifying sites that exhibited materials-related distress, and both were considered to have passed the proof-of-concept trials. However, neither method can currently diagnose materials-related distress. Both techniques only detected the symptoms of materials-related distress; the actual diagnosis still relied on coring and subsequent petrographic examination. Both technologies are currently in rapid development, and the limitations may be overcome as the technologies advance and mature.

In situ RHAMM protein expression in acute myeloid leukemia blasts suggests poor overall survival.

Treatment options for patients with high-risk acute myeloid leukemia (AML) include high-dose chemotherapy regimens in combination with allogeneic hematopoietic stem cell transplantation, which takes advantage of the donor T-cell-mediated graft-versus-leukemia effect. Together with beneficial responses observed in assays targeted at leukemia-associated antigens (LAA), this encouraged research on cancer vaccines and adoptive cellular therapies in AML. The receptor for hyaluronic acid-mediated motility (RHAMM, CD168) was identified as one of the most promising LAA in AML. Thus far, little is known about in situ expression in leukemic bone marrow blasts or the prognostic role of RHAMM and its interaction partners in AML. We immunohistochemically analyzed the expression and prognostic significance of RHAMM on trephine bone marrow biopsies from 71 AML cases that had been evaluated for cytogenetics and presence of FLT3-internal tandem duplications and NPM1 mutations. Fifty-five patients (77%) were treated with curative intent, while 16 (23%) received the most appropriate supportive care. Twenty of 71 (28%) AML cases were considered RHAMM+. Receiver operating characteristic curves showed significant discriminatory power considering overall survival (OS) in AML patients treated curatively for RHAMM (p = 0.015). Multivariable analysis revealed that expression of RHAMM in >5% of leukemic blasts identifies a subgroup of curatively treated cases with adverse OS independent of failures to achieve complete remission. RHAMM not only represents a promising LAA with specific T-cell responses in AML but, if assessed in situ on blasts, also a probable prognostic factor.

In situ and genetic characterization of Gossypium barbadense populations from the states of Pará and Amapá, Brazil

The objective of this work was to characterize the populations of Gossypium barbadense in the states of Amapá and Pará, Brazil. In situ characterization was conducted through interviews with the owners of the plants and environmental observations. Leaf or petal tissue as well as seed samples were collected for genetic characterization by single sequence repeats markers and for storage in germplasm banks, respectively. The plants were maintained in dooryards and used mainly for medical purposes. The genetic analysis showed no heterozygous plants at the loci tested (f = 1), indicating that reproduction occurs mainly through selfing. The total genetic diversity was high (He = 0.39); and a high level of differentiation was observed between cotton plants from the two states (F ST = 0.36). Conventional methods of in situ maintenance of G. barbadense populations are not applicable. The conservation of the genetic variability of populations present in the two states could be achieved through germplasm collection and establishing of ex situ seed banks.

Consells d’extracció i conservació del material arqueològic in situ

Aquest petit treball pretén esdevenir una guia bàsica per aquells arqueòlegs que desconeixen l’aspecte conservatiu dels materials arqueològics. Així, en primer lloc analitzarem, a grans trets, la composició físicoquímica dels diferents objectes que podem trobar en una excavació i quins són els agents que més els malmeten. Després tractarem d’introduir alguns consells pràctics pel treball de camp.

Towards desired crystalline product properties: In-situ monitoring of batch crystallization

The objective of industrial crystallization is to obtain a crystalline product which has the desired crystal size distribution, mean crystal size, crystal shape, purity, polymorphic and pseudopolymorphic form. Effective control of the product quality requires an understanding of the thermodynamics of the crystallizing system and the effects of operation parameters on the crystalline product properties. Therefore, obtaining reliable in-line information about crystal properties and supersaturation, which is the driving force of crystallization, would be very advantageous. Advanced techniques, such asRaman spectroscopy, attenuated total reflection Fourier transform infrared (ATR FTIR) spectroscopy, and in-line imaging techniques, offer great potential for obtaining reliable information during crystallization, and thus giving a better understanding of the fundamental mechanisms (nucleation and crystal growth) involved. In the present work, the relative stability of anhydrate and dihydrate carbamazepine in mixed solvents containing water and ethanol were investigated. The kinetics of the solvent mediated phase transformation of the anhydrate to hydrate in the mixed solvents was studied using an in-line Raman immersion probe. The effects of the operation parameters in terms of solvent composition, temperature and the use of certain additives on the phase transformation kineticswere explored. Comparison of the off-line measured solute concentration and the solid-phase composition measured by in-line Raman spectroscopy allowedthe identification of the fundamental processes during the phase transformation. The effects of thermodynamic and kinetic factors on the anhydrate/hydrate phase of carbamazepine crystals during cooling crystallization were also investigated. The effect of certain additives on the batch cooling crystallization of potassium dihydrogen phosphate (KDP) wasinvestigated. The crystal growth rate of a certain crystal face was determined from images taken with an in-line video microscope. An in-line image processing method was developed to characterize the size and shape of thecrystals. An ATR FTIR and a laser reflection particle size analyzer were used to study the effects of cooling modes and seeding parameters onthe final crystal size distribution of an organic compound C15. Based on the obtained results, an operation condition was proposed which gives improved product property in terms of increased mean crystal size and narrowersize distribution.