Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of platelet refractoriness in oncohematologic patients

OBJECTIVES: To identify the occurrence and the causes of platelet refractoriness in oncohematologic patients. INTRODUCTION: Platelet refractoriness (unsatisfactory post-transfusion platelet increment) is a severe problem that impairs the treatment of oncohematologic patients and is not routinely investigated in most Brazilian services. METHODS: Forty-four episodes of platelet concentrate transfusion were evaluated in 16 patients according to the following parameters: corrected count increment, clinical conditions and detection of anti-platelet antibodies by the platelet immunofluorescence test (PIFT) and panel reactive antibodies against human leukocyte antigen class I (PRA-HLA). RESULTS: Of the 16 patients evaluated (median age: 53 years), nine (56%) were women, seven of them with a history of pregnancy. An unsatisfactory increment was observed in 43% of the transfusion events, being more frequent in transfusions of random platelet concentrates (54%). Platelet refractoriness was confirmed in three patients (19%), who presented immunologic and non-immunologic causes. Alloantibodies were identified in eight patients (50%) by the PIFT and in three (19%) by the PRA-HLA. Among alloimmunized patients, nine (64%) had a history of transfusion, and three as a result of pregnancy (43%). Of the former, two were refractory (29%). No significant differences were observed, probably as a result of the small sample size. CONCLUSION: The high rate of unsatisfactory platelet increment, refractoriness and alloimmunization observed support the need to set up protocols for the investigation of this complication in all chronically transfused patients, a fundamental requirement for the guarantee of adequate management.
Genetic Differences in Transcript Responses to Low-Dose Ionizing Radiation Identify Tissue Functions Associated with Breast Cancer Susceptibility

High dose ionizing radiation (IR) is a well-known risk factor for breast cancer but the health effects after low-dose (LD, <10 cGy) exposures remain highly uncertain. We explored a systems approach that compared LD-induced chromosome damage and transcriptional responses in strains of mice with genetic differences in their sensitivity to radiation-induced mammary cancer (BALB/c and C57BL/6) for the purpose of identifying mechanisms of mammary cancer susceptibility. Unirradiated mammary and blood tissues of these strains differed significantly in baseline expressions of DNA repair, tumor suppressor, and stress response genes. LD exposures of 7.5 cGy (weekly for 4 weeks) did not induce detectable genomic instability in either strain. However, the mammary glands of the sensitive strain but not the resistant strain showed early transcriptional responses involving: (a) diminished immune response, (b) increased cellular stress, (c) altered TGFβ-signaling, and (d) inappropriate expression of developmental genes. One month after LD exposure, the two strains showed opposing responses in transcriptional signatures linked to proliferation, senescence, and microenvironment functions. We also discovered a pre-exposure expression signature in both blood and mammary tissues that is predictive for poor survival among human cancer patients (p = 0.0001), and a post-LD-exposure signature also predictive for poor patient survival (p<0.0001). There is concordant direction of expression in the LD-exposed sensitive mouse strain, in biomarkers of human DCIS and in biomarkers of human breast tumors. Our findings support the hypothesis that genetic mechanisms that determine susceptibility to LD radiation induced mammary cancer in mice are similar to the tissue mechanisms that determine poor-survival in breast cancer patients. We observed non-linearity of the LD responses providing molecular evidence against the LNT risk model and obtained new evidence that LD responses are strongly influenced by genotype. Our findings suggest that the biological assumptions concerning the mechanisms by which LD radiation is translated into breast cancer risk should be reexamined and suggest a new strategy to identify genetic features that predispose or protect individuals from LD-induced breast cancer.
Reproductive biology of Acrolophia cochlearis (Orchidaceae): estimating rates of cross-pollination in epidendroid orchids.

BACKGROUND AND AIMS Pollen fates strongly influence mating success in plants but are difficult to quantify. By promoting foraging constancy in pollinators, floral rewards such as nectar may enhance the overall efficiency of pollen transfer. However, this can also lead to high levels of geitonogamy. Pollen fates were studied in Acrolophia cochlearis, a member of a terrestrial epidendroid orchid genus that includes both rewarding and deceptive species. METHODS Pollinator observations were conducted. Pollen transfer efficiency (PTE), the proportion of removed pollinia deposited on stigmas, was measured in a large population at regular intervals throughout the 5-month flowering season. The level of cross-pollination in two populations was estimated from the percentage of seeds with embryos in naturally pollinated fruits. KEY RESULTS Acrolophia cochlearis (and a congener A. micrantha) produce minute but concentrated nectar rewards. Observations showed that A. cochlearis is pollinated exclusively by a solitary bee species, Colletes claripes. Although both sexes visited flowers, only males carried pollinaria. Overall levels of pollination and PTE of the rewarding A. cochlearis were much higher than in a deceptive congener, A. capensis. Seeds resulting from self-fertilization had a significantly lower probability of containing viable embryos than did those from cross-fertilization. This dichotomy in fruit quality was used to estimate that cross-pollination occurred in approx. 66 % of A. cochlearis flowers in a large dense population and approx. 10 % in a small sparse population. Traits of A. cochlearis that limit geitonogamy include pollinarium reconfiguration that exceeds the visit time of pollinators and rapid flower senescence following visitation. CONCLUSIONS Presence of a nectar reward in Acrolophia cochlearis results in high levels of PTE. It is estimated that approx. 33-90 % of fruits in natural populations arise from self-pollination in this species.
Effects on academic learning of manipulating emotional states and motivational dynamics.

SUMMARY. The aim of this study was to investigate the effects of emotionally disturbing stimuli on the learning process. A five-minute film segment depicting horrific scenes of automobile accident victims, and part of a pathologist’s post-mortem of a victim, was shown to an experimental group of 69 student teachers, while a non-treatment group of 66 student teachers served as controls. The two groups were well matched on several independent variables covering the four domains of ability, personality, motivation, and mood states. The emotionally disturbing treatment produced a decrement in learning performance, but resulted in a massive 36 per cent increase in predictive variance attributable to enhanced correlations between the non-ability intrapersonal variables and learning performance, for a prose learning task.
An Adaptive Multi-agent Organization Model Based on Dynamic Role Allocation

Organizations involving multiple agents require adaptation mechanisms to guarantee robustness, especially in critical domains. A template is presented for analysis and design of organizations with adaptation by dynamic role reallocation. This adaptive organization model can be used both for qualitative and quantitative domains, shown in two application cases made to evaluate the applicability of the model.
Automatic construction of clean broad-coverage translation lexicons

Word-level translational equivalences can be extracted from parallel texts by surprisingly simple statistical techniques. However, these techniques are easily fooled by {\em indirect associations} --- pairs of unrelated words whose statistical properties resemble those of mutual translations. Indirect associations pollute the resulting translation lexicons, drastically reducing their precision. This paper presents an iterative lexicon cleaning method. On each iteration, most of the remaining incorrect lexicon entries are filtered out, without significant degradation in recall. This lexicon cleaning technique can produce translation lexicons with recall and precision both exceeding 90\%, as well as dictionary-sized translation lexicons that are over 99\% correct.
Impact Analysis : a Semi-Automated Technique and Associated Tool

This paper presents a technique, and associated tool, for supporting the analysis of the impacts of changes on software systems. The approach is to exploit the dependencies that exist within the somare system to be modified, modelled as a graph of objects and links. Changes are modelled as events that are propagated upon the graph according to predefined propagation rules. To cover situations in which a deeper analysis is required, it is possible to define potential propagation rules; the impacts of such rules are then declared as potential and a human decision is required to check whether they are real or not. The associated tool encompasses a propagation engine, which implements the automatic propagation of impacts, and a set of user oriented features supporting the control of the propagation engine and providing an highly interactive user interface for analysing the results of the automatic propagation.
MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks

Summary: We developed MolBioLib to address the need for adaptable next-generation sequencing analysis tools. The result is a compact, portable and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. MolBioLib is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib has been used to identify causative single-nucleotide polymorphisms in whole genome sequencing, detect balanced chromosomal rearrangements and compute enrichment of messenger RNAs (mRNAs) on microtubules, typically requiring applications of under 200 lines of code. MolBioLib includes programs to perform a wide variety of analysis tasks, such as computing read coverage, annotating genomic intervals and novel peak calling with a wavelet algorithm. Although MolBioLib was designed primarily for bioinformatics purposes, much of its functionality is applicable to a wide range of problems. Complete documentation and an extensive automated test suite are provided. Availability: MolBioLib is available for download at: http://sourceforge.net/projects/molbiolib Contact: ohsumit@molbio.mgh. harvard.edu
Location of T cell and major histocompatibility complex antigens in the human thymus

A series of monoclonal antibodies were used to study the intrathymic distribution of T cell-specific antigens, Ia antigens, and beta 2- microglobulin in frozen sections of human thymus by immunofluorescence and immunoperoxidase techniques. Most of the cortical thymocytes reacted with anti-T4, anti-T5, anti-T6, anti-T8, and anti-T10 antibodies, thus indicating coexpression of multiple antigens on cortical lymphocytes. The staining of cells in the medulla was most satisfactorily judged in sections stained with the immunoperoxidase technique. Many medullary cells reacted with anti-T4--and a smaller fraction with anti-T5, anti-T6, anti-T8, and anti-T10 antibodies. In addition, T1 and T3 antibodies, which react with all peripheral T cells, stained a majority of medullary cells. The medullary cells were also more intensely stained with antibodies directed against beta 2- microglobulin than the majority of cortical cells. Hence, the staining profile of medulla approximates the staining pattern of peripheral T cells, with large numbers of cells bearing T1+, T3+, and T4+ antigens (helper/inducer cells) and a small number of cells bearing T1+, T3+, and T5+/T8+ antigens (suppressor/cytotoxic cells). This supports the conclusion that mature cells present in the medulla are derived from immature cells in the cortex. However, a small number of cells scattered throughout the cortex stained with T1 and T3 antibodies, which suggests that maturation of thymocytes can also occur in the cortex. Antibody directed against Ia antigens resulted in a characteristic patchy pattern of staining in the cortex and in diffuse staining in the medulla, which was interpreted as resulting from staining of epithelial reticulum. The majority of thymocytes did not stain. The staining pattern suggests a close relationship between epithelial cells and thymocytes.
A Learning Style Perspective to Investigate the Necessity of Developing Adaptive Learning Systems

Learning styles are considered to be one of the factors that need to be taken into account in developing adaptive learning systems. However, few studies have been conducted to investigate if students have the ability to choose the best-fit e-learning systems or content presentation styles for themselves in terms of learning style perspective. In this paper, we aim to investigate these issues by using two versions of an educational game developed based on the sequential/global dimension of the learning style proposed by Felder and Silverman. The experimental results showed that the choices made by the students were not related to their cognitive process or learning style; instead, most students made their choices by intuition based on personal preferences. Moreover, the students who learned with learning style-fit versions showed significantly better learning achievement than those who learned with non-fit versions. Consequently, it is concluded that students preferring one game over another does not necessarily mean that they will learn better with that version, revealing the importance and necessity of developing adaptive learning systems based on learning styles.
Evidence that transmitter‐containing dystrophic neurites precede paired helical filament and Alz‐50 formation within senile plaques in the amygdala of nondemented elderly and patients with Alzheimer's disease

Immunocytochemical techniques were employed to examine the temporal ordering whereby amyloid β‐protein (AβP) and neuronal elements collectively come together to form senile plaques in Alzheimer's disease (AD). Specifically, we addressed three questions: (1) whether AβP deposition precedes or follows neuritic changes; (2) whether paired helical filament (PHF) formation is an early or late event in the genesis of the dystrophic neurites which participate in plaque formation; and (3) whether the density of senile plaques displays any relationship with the prevalence of PHF or Alz‐50 containing neurons. To address these questions we studied the amygdala from a group of patients with AD, a group of nondemented age‐matched individuals exhibiting a sufficient number of senile plaques to be classified by neuropathological criteria as AD, and a group of age‐matched controls without AD pathology. Amyloid‐bearing plaques were demonstrated by AβP immunolabeling and thioflavine‐S staining. Neuritic changes in the form of dystrophic neurites were observed with the aid of antibodies against PHF, Alz‐50, as well as antibodies against several neuropeptides (i.e., substance P, somatostatin, and neurotensin) and the acetylcholine biosynthetic enzyme, choline acetyltransferase.
Characterizing the function and structural organization of the 5′ tRNA-like motif within the hepatitis C virus quasispecies

Hepatitis C virus (HCV) RNA is recognized and cleaved in vitro by RNase P enzyme near the AUG start codon. Because RNase P identifies transfer RNA (tRNA) precursors, it has been proposed that HCV RNA adopts structural similarities to tRNA. Here, we present experimental evidence of RNase P sensitivity conservation in natural RNA variant sequences, including a mutant sequence (A368–G) selected in vitro because it presented changes in the RNA structure of the relevant motif. The variation did not abrogate the original RNase P cleavage, but instead, it allowed a second cleavage at least 10 times more efficient, 4 nt downstream from the original one. The minimal RNA fragment that confers sensitivity to human RNase P enzyme was located between positions 299 and 408 (110 nt). Therefore, most of the tRNA-like domain resides within the viral internal ribosome entry site (IRES) element. In the variant, in which the mutation stabilizes a 4 nt stem–loop, the second cleavage required a shorter (60 nt) substrate, internal to the minimal fragment substrate, conforming a second tRNA-like structure with similarities to a ‘Russian-doll’ toy. This new structure did not impair IRES activity, albeit slightly reduced the efficiency of translation both in vitro and in transfected cells. Conservation of the original tRNA-like conformation together with preservation of IRES activity points to an essential role for this motif. This conservation is compatible with the presence of RNA structures with different complexity around the AUG start codon within a single viral population (quasispecies).
Campaigns for lazy voters: truncated ballots

We study elections in which voters may submit partial ballots consisting of truncated lists: each voter ranks some of her top candidates (and possibly some of her bottom candidates) and is indifferent among the remaining ones. Holding elections with such votes requires adapting classical voting rules (which expect complete rankings as input) and these adaptations create various opportunities for candidates who want to increase their chances of winning. We provide complexity results regarding planning various kinds of campaigns in such settings, and we study the complexity of the possible winner problem for the case of truncated votes.
Community Standards for Arabidopsis Genetics Originally given to Mutants Defective in Phytochrome A

in expanding databases, and efficiency in multinational research programs. Examples of problems The Netherlands The need for coordination of Arabidopsis nomenclature became apparent in the late 1980s as investigators began isolating large numbers of mutants and assigning them Introduction gene symbols without knowledge of related activities in The explosive growth of Arabidopsis research over the other laboratories. This resulted in the same symbol occa-past 15 years has brought about fundamental changes in sionally being used for mutants with completely different the nature of basic plant research. It has also created a phenotypes. A case in point was the publication, in succes-number of serious challenges for plant biologists with sive issues of the same journal, of phenotypic descriptions respect to coordination of research efforts. The Arabidopsis of two unrelated sin mutants. One exhibited a short integu-community has responded to these challenges by estab-ment in the ovule (Robinson-Beers et al., 1992). The other lishing an effective network of national and multinational was defective in sinapic acid biosynthesis (Chapple et al., research programs, advisory committees, and workshops 1992). This prompted the establishment of a common list designed to foster coordination and cooperation. The elec-of mutant gene symbols that was distributed to community tronic Arabidopsis news group, initiated ten years ago to members for consultation before publication of new sym-enhance rapid communication among research groups bols. This system has expanded to an Internet format in worldwide, and the Multinational Arabidopsis Genome recent years (http://mutant.lse.okstate.edu/) and has Research Project, established in 1990 to stimulate and reduced but not eliminated the accidental selection of coordinate research efforts in plant molecular genetics, identical symbols. are two models of community organization that have A second problem has been the assignment of different subsequently been applied to other organisms. names and symbols to mutant alleles of the same gene, Establishing standards for nomenclature, mapping and or in some cases even the same allele. There have been genetic analysis in Arabidopsis has also required com-several reasons for this confusion. One has been the failure munity organization. The importance of such standards to recognize that certain phenotypes are related. A good has been discussed in the past, and some coordination example was the discovery that cytokinin-insensitive (ckr1) has been achieved through monographs (Meyerowitz and and ethylene-insensitive (ein2) mutants, each characterized Somerville, 1994), conferences and the Internet, but without from different perspectives in different laboratories published guidelines it has been difficult to …
Using implicit associations towards fruit consumption to understand fruit consumption behaviour and habit strength relationships

An implicit association test (IAT) was used to investigate how habit strength, implicit attitudes and fruit consumption interrelate. Fifty-two participants completed a computerized IAT and provided measures of fruit consumption and related habit strength. Implicit attitudes moderated the habit strength—fruit consumption relationship; stronger relationships were observed when implicit attitudes were more positive. Amongst those with strong fruit habits, more positive associations with fruit were found for those who had recently consumed sufficient fruits compared to those who had not. Findings demonstrate the relevance of implicit positive associations in understanding the relationship between fruit consumption habits and subsequent fruit consumption.
Preoperative Gadoxetic Acid-Enhanced MRI and Simultaneous Treatment of Early Hepatocellular Carcinoma Prolonged Recurrence-Free Survival of Progressed Hepatocellular Carcinoma Patients after Hepatic Resection

Background/Purpose. The purpose of this study was to clarify whether preoperative gadoxetic acid-enhanced magnetic resonance imaging (EOB-MRI) and simultaneous treatment of suspected early hepatocellular carcinoma (eHCC) at the time of resection for progressed HCC affected patient prognosis following hepatic resection. Methods. A total of 147 consecutive patients who underwent their first curative hepatic resection for progressed HCC were enrolled. Of these, 77 patients underwent EOB-MRI (EOB-MRI (+)) before hepatic resection and the remaining 70 patients did not (EOB-MRI (−)). Suspected eHCCs detected by preoperative imaging were resected or ablated at the time of resection for progressed HCC. Results. The number of patients who underwent treatment for eHCCs was significantly higher in the EOB-MRI (+) than in the EOB-MRI (−) (17 versus 6; P = 0.04). Recurrence-free survival (1-, 3-, and 5-year; 81.4, 62.6, 48.7% versus 82.1, 41.5, 25.5%, resp., P < 0.01), but not overall survival (1-, 3-, and 5-year; 98.7, 90.7, 80.8% versus 97.0, 86.3, 72.4%, resp., P = 0.38), was significantly better in the EOB-MRI (+). Univariate and multivariate analyses showed that preoperative EOB-MRI was one of the independent factors significantly correlated with better recurrence-free survival. Conclusions. Preoperative EOB-MRI and simultaneous treatment of eHCC prolonged recurrence-free survival after hepatic resection.