Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytogenetic patterns in ETV6/RUNX1‐positive pediatric B‐cell precursor acute lymphoblastic leukemia: A Nordic series of 245 cases and review of the literature

Between 1992 and 2004, 1,140 children (1 to <15 years) were diagnosed with B‐cell precursor acute lymphoblastic leukemia (ALL) in the Nordic countries. Of these, 288 (25%) were positive for t(12;21)(p13;q22) [ETV6/RUNX1]. G‐banding analyses were successful in 245 (85%); 43 (15%) were karyotypic failures. The modal chromosome numbers, incidence, types, and numbers of additional abnormalities, genomic imbalances, and chromosomal breakpoints in the 245 karyotypically informative cases, as well as in 152 previously reported cytogenetically characterized t(12;21)‐positive ALLs in the same age group, were ascertained. The most common modal numbers among the 397 cases were 46 (67%), 47 (16%), 48 (6%), and 45 (5%). High‐hyperdiploidy, triploidy, and tetraploidy were each found in ∼1%; none had less than 40 chromosomes. Secondary chromosomal abnormalities were identified by chromosome banding in 248 (62%) of the 397 ALLs. Of these, 172 (69%) displayed only unbalanced changes, 14 (6%) only balanced aberrations, and 26 (10%) harbored both unbalanced and balanced abnormalities; 36 (15%) were uninformative because of incomplete karyotypes. The numbers of secondary changes varied between 1 and 19, with a median of 2 additional aberrations per cytogenetically abnormal case. The most frequent genomic imbalances were deletions of 6q21‐27 (18%), 8p11‐23 (6%), 9p13‐24 (7%), 11q23‐25 (6%), 12p11‐13 (27%), 13q14‐34 (7%), loss of the X chromosome (8%), and gains of 10 (9%), 16 (6%), and 21 (29%); no frequent partial gains were noted. The chromosome bands most often involved in structural rearrangements were 3p21 (2%), 5q13 (2%), 6q12 (2%), 6q14 (2%), 6q16 (2%), 6q21 (10%), 6q23 (6%), 6q25 (3%), 9p13 (2%), 11q13 (2%), 11q23 (2%), 12p11 (6%), 12p12 (7%), 12p13 (25%), 21q10 (6%), and 21q22 (6%). Considering that the t(12;21) is known to arise in utero and that the postnatal latency period is protracted, additional mutations are most likely necessary for overt ALL. The frequently rearranged chromosome regions may harbor genes of importance for the transformation and/or progression of an initial preleukemic t(12;21)‐positive clone. © 2007 Wiley‐Liss, Inc.
Skipjack Tuna Availability for Purse Seine Fisheries Is Driven by Suitable Feeding Habitat Dynamics in the Atlantic and Indian Oceans

An Ecological Niche model was developed for skipjack tuna (Katsuwonus pelamis, SKJ) in the Eastern Central Atlantic Ocean (AO) and Western Indian Ocean (IO) using an extensive set of presence data collected by the European purse seine fleet (1998 – 2014). Chlorophyll-a fronts were used as proxy for food availability while mixed layer depth, sea surface temperature, dissolved oxygen, salinity, current intensity and height anomaly variables were selected to describe SKJ’s abiotic environmental preferences. The resultant ecological niche included both mesoscale eddy-type productive features that displayed latitudinal range in the IO to large scale upwelling systems that shrink and swell seasonally in the AO. Overall, 83% of all free swimming school sets (FSC) and 75% of drifting fish aggregating device sets (dFAD) that contained SKJ occurred within 25 km of favorable feeding habitat. In the AO, 34% of dFAD sets were made more than 100 km away from this habitat, mostly in the surface chlorophyll-a poor environment of the Guinea Current. These distant sets represent 10% of dFAD sets in the IO and 8% of all FSC sets. Our results suggest that the Mozambique Channel in the IO, with its simultaneously favorable feeding and spawning conditions, may seasonally offer a better SKJ nursery habitat than the Guinea Current which shows a substantially poorer feeding capacity. With the exception of this latter area, our results also suggest that fishing accessibility will be higher in months where the size of the favorable feeding habitats are reduced, likely because this reduction drives a geographical contraction in SKJ populations. The observed relationship between the annual size of favorable feeding habitat and both annual catch rates and total catches in the IO is consistent with the near-full exploitation of this stock that has occurred since the 2000s. Moreover, it suggests that annual habitat size could be used as an indicator of growth capacity for this highly productive stock. Habitat monitoring, as part of a dynamic fisheries management approach, should contribute to the sustainable exploitation of SKJ by providing information on the climate-dependent aspects of stock variability and the effects of dFAD deployment in food-rich habitats.
The role of semen in induction of maternal immune tolerance to pregnancy.

Successful pregnancy requires a state of maternal immune 'tolerance' to accommodate antigens expressed by the conceptus. Implantation failure and placental pathologies largely reflect insufficiencies in maternal immune adaptation, but progress in devising therapeutic strategies to treat these conditions is stalled because the mechanisms underlying the induction and maintenance of maternal tolerance are unknown. Increasingly, clinical and experimental data support the proposal that insemination has consequences for the reproductive process beyond delivery of male gametes. An emerging hypothesis, based mainly on clinical observations and experiments in mice, is that insemination is causally linked to the activation and expansion of populations of lymphocytes mediating forms of 'active' immune tolerance in the implantation site. This review examines existing evidence for a role for semen in the immunology of pregnancy, highlighting the limitations of our existing knowledge and the prospects for future research and its clinical application.
Effect of growth hormone treatment on adult height of children with idiopathic short stature. Genentech Collaborative Group.

BACKGROUND Short-term administration of growth hormone to children with idiopathic short stature results in increases in growth rate and standard-deviation scores for height. However, the effect of long-term growth hormone therapy on adult height in these children is unknown. METHODS We studied 121 children with idiopathic short stature, all of whom had an initial height below the third percentile, low growth rates, and maximal stimulated serum concentrations of growth hormone of at least 10 microg per liter. The children were treated with growth hormone (0.3 mg per kilogram of body weight per week) for 2 to 10 years. Eighty of these children have reached adult height, with a bone age of at least 16 years in the boys and at least 14 years in the girls, and pubertal stage 4 or 5. The difference between the predicted adult height before treatment and achieved adult height was compared with the corresponding difference in three untreated normal or short-statured control groups. RESULTS In the 80 children who have reached adult height, growth hormone treatment increased the mean standard-deviation score for height (number of standard deviations from the mean height for chronologic age) from -2.7 to -1.4. The mean (+/-SD) difference between predicted adult height before treatment and achieved adult height was +5.0+/-5.1 cm for boys and +5.9+/-5.2 cm for girls. The difference between predicted and achieved adult height among treated boys was 9.2 cm greater than the corresponding difference among untreated boys with initial standard-deviation scores of less than -2, and the difference among treated girls was 5.7 cm greater than the difference among untreated girls. CONCLUSION Long-term administration of growth hormone to children with idiopathic short stature can increase adult height to a level above the predicted adult height and above the adult height of untreated historical control children.
Supply chains efficiency increasing based on the modelling of logistics operations

For evaluating the integrated supply chains' (SCs) effective functioning, some new criteria are frequently used apart from the total logistics costs (TLC). These criteria characterise the quality and reliability of accomplishing logistics operations and functions. It is obvious that these metrics are connected and their separate representation is a consequence of not enough developed supply chains' theoretic model and, accordingly, analytical tools allowing carrying out a comprehensive assessment of these metrics. The paper presents the critical analysis of the existing approaches to the TLC evaluation and SC reliability, the methodical approach which allows evaluating the total costs indexes and supplying chains reliability. This approach includes, firstly, the equation of the total logistics costs; secondly, the reliability evaluation model of a simple supply chain which is a reserved system with a renewal; thirdly, a complex of models for the evaluation of the reliability of basic logistics operations (purchase, order processing, choice of intermediaries, transportation, warehouse placement and storage). As most indicators which describe the chain functioning are random values, to obtain the required evaluations there is a developed algorithm based on simulation.
Hypertension associée aux sténoses de l'artère rénale et aux atteintes rénales parenchymateuses

Les sténoses de l’artère rénale peuvent induire une hypertension rénovasculaire mais il s’agit d’une cause rare d’hypertension artérielle (HTA). Elles sont plus fréquentes dans certaines populations d’hypertendus : HTA sévère, récente, du sujet jeune. On distingue plus particulièrement les sténoses athéroscléreuses survenant chez des sujets avec une maladie cardiovasculaire diffuse, et les lésions de dysplasie fibromusculaire qui surviennent en l’absence de facteur de risque cardiovasculaire et typiquement chez des femmes d’âge jeune ou moyen. Le traitement des sténoses athéroscléreuses s’est simplifié ces dix dernières années : il repose principalement sur la prise en charge globale de la maladie cardiovasculaire avec comme trépied thérapeutique l’association d’un antiagrégant plaquettaire, d’un bloqueur du système rénine–angiotensine–aldostérone et d’une statine. Les indications de revascularisation sont rares et doivent être décidées au cas par cas. Les lésions de dysplasie fibromusculaire relèvent d’une surveillance et pour certaines, en particulier les sténoses unifocales, d’une revascularisation par angioplastie, qui permet le plus souvent la baisse de la pression artérielle et, parfois, la guérison de l’HTA. De par leur rôle fondamental dans la régulation de la pression artérielle, les reins sont fréquemment impliqués dans l’HTA. Dans certains cas rares, l’HTA peut être secondaire à une maladie rénale unilatérale dont le traitement peut parfois permettre de guérir l’HTA. Beaucoup plus fréquemment, il s’agit de maladies rénales bilatérales, aiguës ou chroniques nécessitant, outre la prise en charge étiologique, selon les circonstances, la prescription de bloqueurs du système rénine–angiotensine–aldostérone et de diurétiques à dose adaptée à la fonction rénale. Un traitement efficace est d’autant plus important que l’HTA est un facteur de progression de la maladie rénale chronique.
Generating and Approximating Nondominated Coteries

A coterie, which is used to realize mutual exclusion in a distributed system is a family C of incomparable subsets such that every pair of subsets in C has at least one element in common. Associate with a family of subsets C a positive (i.e., monotone) Boolean function f/sub c/ such that f/sub c/(x)=1 if the Boolean vector x is equal to or greater than the characteristic vector of some subset in C, and 0 otherwise. It is known that C is a coterie if and only if f/sub c/ is dual-minor, and is a nondominated (ND) coterie if and only if f/sub c/ is self-dual. We introduce an operator /spl rho/, which transforms a positive self-dual function into another positive self-dual function, and the concept of almost-self-duality, which is a close approximation to self-duality and can be checked in polynomial time (the complexity of checking positive self-duality is currently unknown). After proving several interesting properties of them, we propose a simple algorithm to check whether a given positive function is self-dual or not. Although this is not a polynomial algorithm, it is practically efficient in most cases. Finally, we present an incrementally polynomial algorithm that generates all positive self-dual functions (ND coteries) by repeatedly applying p operations. Based on this algorithm, all ND coteries of up to seven variables are computed. >
Stem cell research: current uses and future challenges

Dear Reader, Long before the existence of stem cells was proven, work with blood islands pointed to the ability of hemangioblasts to generate blood cells in the embryo. Stem cell research has known a dramatic leap forward with the development of embryonic stem cell lines from isolated cells from the inner cell mass of early embryos. Indeed, stem cells have demonstrated to be exciting tools that would permit the unlimited repair and replacement of abnormal, damaged, or absent cell types and tissues (Thomson et al. 1998). A second major breakthrough came when Yamanaka’s group showed the production of induced pluripotent stem cells from adult stem cells upon lentiviral introduction of four transcription factors (Takahashi and Yamanaka 2006), circumventing the ethical controversies associated with deriving stem cells from embryos as pointed out in the review from Schotanus et al. (this issue). In the first review article appearing in this issue, Schauwer et al. (this issue) explore, among others, the applications for bone-marrow-derived mesenchymal stem cells and adipose-derived stromal vascular fraction cells in the treatment of musculoskeletal pathologies that are currently in use in horses. The differential efficacies of various approaches are still being investigated. Further optimization of stem-cell-based therapies should focus on cellular origin, isolation, enrichment, and processing as well as on the timing, route of administration, formulation, and dosing. We still have a long way to go before reaching a full understanding of stem cell biology and translation of these findings into the clinic. Efforts to characterize the molecular mechanisms responsible for the variability encountered between human embryonic stem cells and induced pluripotent stem cell lines have initially focused on expression level variations in protein-coding genes. In addition, Lammens et al. (this issue) explore various recent studies providing evidence that also long non-coding RNAs (regulatory RNA not translated into protein) are key regulators in the maintenance of the stem cell pluripotent state. Finally, it is of great concern, as described in De Bakker et al. (this issue), that little information is available regarding short-term and long-term safety of stem cell therapy in veterinary medicine. These authors point out that a few studies in horses and dogs have currently investigated the possible adverse reactions, such as increased thickening of the injured region after mesenchymal stem cell injection and the tumorigenic potential. I hope the readers of Veterinary Quarterly will enjoy reading these informative articles as much as I have.
Aromatic-aromatic interactions in and around alpha-helices.

To understand the role of aromatic-aromatic interactions in imparting specificity to the folding process, the geometries of four aromatic residues with different sequence spacing, located in alpha-helices or five residues from helical ends, interacting with each other have been elucidated. The geometry is found to depend on the sequence difference. Specific interactions (C-H.pi and N-H.pi) which result from this geometry may cause a given pair of residues (such as Phe-His) with a particular sequence difference to occur more than expected. The most conspicuous residue in an aromatic pair in the context of helix stability is His, which is found at the last (C1) position or the two positions (Ncap and Ccap) immediately flanking the helix. An alpha-helix and a contiguous 3(10)-helix or two helices separated by a non-helical residue can have interacting aromatic pairs, the geometry of interaction and the relative orientation between the helices being rather fixed. Short helices can also have interacting residues from either side.
Hybrid specification of control systems

An alternative approach to the development of control systems is presented. It differs from current ones in two aspects, because it is based on a formal software specification language, which allows formal verification and because it enables multidisciplinary development of a control system as existing control models can be easily incorporated in the discussed approach. Simulation of ASTRAL specifications is discussed. Simulation, as opposed to verification which is laborious, is useful to provide a quick impression of possible system behaviors. It is shown how existing (continuous) control models, like those constructed using software packages like MatLab, can be incorporated in an ASTRAL specification thus leading to a hybrid specification containing both continuous and discrete subsystems. This hybrid style of specification is illustrated by the example of a robot control system. The specification language and some aspects of control theory are discussed in the introduction. In the second section the example specification concerning robot control and incorporation of continuous system models is discussed. Simulation of the specification is addressed in the third section. The final section presents conclusions and suggestions for future work.
Mutational analysis of the trans-activation-responsive region of the human immunodeficiency virus type I long terminal repeat

We used site-directed mutagenesis to delineate sequences within the human immunodeficiency virus type I (HIV-I) long terminal repeat (LTR) required for trans-activation by the viral tat gene product. We demonstrated that sequences 3' to LTR position +44 are dispensable for trans-activation but that almost all of the mutations tested located between positions -17 and +44 greatly reduced trans-activation at both the transcriptional and posttranscriptional levels. However, displacement of the HIV-I LTR trans-activation-responsive region (TAR) 3' by insertion of up to 32 base pairs between the LTR TATA box and cap site had little effect on trans-activation. An analysis of the DNase I hypersensitivity profile of the HIV-I LTR in transfected cultures suggested the presence of at least two DNase I-hypersensitive sites, including one which extends into the viral TAR element; however, neither of these sites appeared to be significantly affected by tat coexpression. These results allow more precise delineation of the sequences important for TAR function and suggest that the TAR may be recognized by a host-specific DNA-binding protein rather than by the tat protein directly.
Molecular and functional changes of pulmonary surfactant in response to hyperoxia

Surfactant comprises phosphatidylcholine (PC) together with anionic phospholipids, neutral lipids, and surfactant proteins SP‐A to‐D. Its composition is highly specific, with dipalmitoyl‐PC, palmitoyl‐myristoyl‐PC, and palmitoyl‐palmitoleoyl‐PC as its predominant PC species, but with low polyunsaturated phospholipids. Changes in pulmonary metabolism and function in response to injuries depend on their duration and whether adaptation can occur. We examined in rats prolonged (7 days) versus acute (2 days) exposure to non‐lethal oxygen concentrations (85%) with respect to the composition and metabolism of individual lung phospholipid molecular species. Progressive inflammation, structural alteration, and involvement of type II pneumocytes were confirmed by augmented bromodeoxyuridine incorporation, broadening of alveolar septa, and increased granulocyte, macrophage, SP‐A, and SP‐D concentrations. Surfactant function was impaired after 2 days, but normalized with duration of hyperoxia, which was attributable to inhibition but not to alteration in SP‐B/C concentrations. Phospholipid pool sizes and PC synthesis by lung tissue, as assessed by [methyl‐3H]‐choline incorporation, were unchanged after 2 days, although after 7 days they were elevated 1.7‐fold. By contrast, incorporation of labeled PC into tissue pools of surfactant and lung lavage fluid decreased progressively. Moreover, concentrations of arachidonic acid containing phospholipids were augmented at the expense of saturated palmitoyl‐myristoyl‐PC and dipalmitoyl‐PC. We conclude a persisting impairment in the intracellular trafficking and secretion of newly synthesized PC, accompanied by a progressive increase in alveolar arachidonic acid containing phospholipids in spite of recovery of acutely impaired surfactant function and adaptive increase of overall PC synthesis. Pediatr Pulmonol. 2006, 41:1025–1039. © 2006 Wiley‐Liss, Inc.
Le rôle de la logistique dans le développement de nouveaux produits

Pour de nombreuses firmes, la réussite d’un projet de développement de nouveaux produits (DNP) est essentielle à la stratégie de l’entreprise. Or le rôle de la logistique dans ces projets a rarement été étudié. Ce papier teste empiriquement la relation entre logistique et développement de nouveaux produits et les améliorations de la performance des projets DNP et la performance de la logistique. Des directeurs logistique d’entreprises industrielles américaines ont été intérrogés. L’analyse montre que la performance du projet DNP et la performance de la logistique du projet s’est accrue avec l’implication de la fonction logistique dans le développement de nouveaux produits.
UTX 1.11, a Simple and Open User Dictionary/Terminology Standard, and its Effectiveness with Multiple MT Systems

We have formulated a dictionary/glossary format UTX 1.11 and released it in May 2011. UTX 1.11 is a simple format that is friendly to both computers and humans. UTX dictionaries can be used not only as machinereadable dictionaries for rule-based machine translation (MT) systems, but also for computer-aided translation by human translators. The initial objective of UTXSimple 1.00, released in 2008, was to improve the accuracy of various MT systems by specifying a common format. A key feature of its latest version UTX 1.11 is a term management mechanism by introducing four term statuses ("provisional," "forbidden," "approved," and "non-standard"). We show that a UTX 1.11-based dictionary originally created as a glossary is highly effective for improving the accuracy of MT. UTX can be widely and successfully applied in various fields with specialized terminology, such as localization, open source, education, administration, medicine, and law.
On dying and human suffering

This review compares and contrasts the major reoccurring themes in two sources of research literature – social studies of dying and human suffering. The purpose of such a comparison is to employ the major insights of each field as a useful method of critically evaluating the insights of the other. Critical exchanges and comparisons between the research area of dying studies and on human suffering have been modest to date. This article will explain that the experience of dying benefits from being situated and analysed in a broader context of cultural experience, as suggested by the theory and study of human suffering. Conversely, the theory and methods involved in studies of human suffering can gain from a mortal view of vulnerability, grief, social ambiguity and identity changes characteristic of experiences at the end of life.