Miracle-dz/UniFAR-FTUs huggingface dataset:
Oncological outcome and prognostic factors in the therapy of soft tissue sarcoma of the extremities

Uniform conclusions about therapeutic concepts and survival time of bone and soft tissue sarcoma patients are difficult due to the heterogeneity of histological subtypes as well as the different responses to neoadjuvant therapy. The subject of this retrospective study was the analysis of tumour free survival, risk and prognostic factors of sarcoma patients treated by limb sparing techniques or amputation. We included 118 patients with soft tissue sarcoma of the extremities treated primarily or secondarily at our institution between 1990 and 2008 with a minimum follow-up of 12 months. Data about the tumour free survival time, operative techniques and potential prognostic factors were analysed. The tumour-specific and overall survival were significantly influenced by two factors: the grading and distant metastases present at time of diagnosis. Optimal multimodal therapeutic concepts at a specialized Cancer Center decreased the risk of local recurrence. The importance of optimal preoperative and surgical course concerning the oncological long term outcome was investigated. The decrease in local recurrence as a result of multimodal therapeutic concepts at a specialized Cancer Center was confirmed. To evaluate the individual prognosis of a patient, multiple factors have to be considered. Factors for a poor prognosis are primary metastasis, high-grade tumours and several histological entities (e.g. synovial sarcoma, not other specified).
Evaluating Stages of Development in Second Language French: A Machine-Learning Approach

This paper describes a system to define and evaluate development stages in second language French. The identification of such stages can be formulated as determining the frequency of some lexical and grammatical features in the learners’ production and how they vary over time. The problems in this procedure are threefold: identify the relevant features, decide on cutoff points for the stages, and evaluate the degree of success of the model. The system addresses these three problems. It consists of a morphosyntactic analyzer called Direkt Profil and a machine-learning module connected to it. We first describe the usefulness and rationale behind its development. We then present the corpus we used to develop the analyzer. Finally, we present new and substantially improved results on training machine-learning classifiers compared to previous experiments (Granfeldt et al., 2006). We also introduce a method to select attributes in order to identify the most relevant grammatical features. (Less)
Comparative Metagenomics of Microbial Communities

The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
Thrombin Generation in the Glasgow Myocardial Infarction Study

Background Thrombin is a key protease in coagulation also implicated in complex pathology including atherosclerosis. To address the role of thrombin in relation to myocardial infarction (MI) we explored thrombin generation analysis in plasma from patients and controls that had participated in the Glasgow MI Study (GLAMIS). Methods Thrombin generation at 1 and 2 pM TF and with and without thrombomodulin (TM) was performed on plasmas from 356 subjects (171 cases, 185 age and sex matched controls) from GLAMIS collected between 3 and 9 months after the MI event. Results Although thrombin generation was slightly delayed in cases (lag time increased from 3.3 to 3.6 min) at the highest trigger, the overall potential to generate thrombin was increased by 7% for the ETP and by 15% for the peak height (both at the 1 pM TF trigger) in cases. Addition of TM did not reveal differences. Furthermore, an increased thrombin generation was associated with MI [normalized ETP: adjusted OR for the highest percentile = 2.4 (95% CI 1.3–4.5) and normalized peak height: adjusted OR = 2.6 (1.3–5.0)] at the lowest trigger; normalized ETP and peak height being 2.1 (1.1–3.8) and 2.0 (1.0–4.1) at the higher 2 pM trigger. Conclusion In GLAMIS, patients with a previous MI had an increased thrombin generation compared to controls. The absence of a clear difference in TM reduction suggests an unaltered anticoagulant activity in these patients. Further research is needed in order to unravel the underlying mechanisms of enhanced thrombin generation after MI.
Search space boundaries in neural network error landscape analysis

Fitness landscape analysis encompasses a selection of techniques designed to estimate the properties of a search landscape associated with an optimisation problem. Applied to neural network training, fitness landscape analysis can be used to establish the link between the shape of the objective function and various neural network design and architecture properties. However, most fitness landscape analysis metrics rely on search space sampling. Since neural network search space is unbounded, it is unclear what subset of the search space should be sampled to obtain representative measurements. This study analyses fitness landscape properties of neural networks under various search space boundaries, and proposes meaningful search space bounds for neural network fitness landscape analysis.
How to Assess Drugs in the Treatment of Acute Bipolar Mania?

Bipolar affective disorder is a serious mental disease associated with significant morbidity and mortality. Good-quality research available to guide treatment strategies remains insufficient, particularly with regard to manic or hypomanic episodes. A critical review of the various stages of mania might be helpful for pharmaceutical companies and investigators as a prerequisite for the clinical evaluation of potential antimanic properties of medications. The main difficulty is with a comparison between anticonvulsants, antipsychotics, and mood stabilizers such as lithium (with equal efficacy in the acute phase and the prevention of recurrent manic episodes). No consensus has been reached with regard to the treatment of bouts of acute mania in various parts of the world. Controlled clinical trials have, at last, provided irrefutable evidence of the activity of lithium, which has long been used alone, as well as that of divalproate or its derivatives and, to a lesser extent, carbamazepine. The new antipsychotic agents have more recently established their efficacy, especially aripiprazole, asenapine, quetiapine; olanzapine, risperidone, and ziprasidone (not sure where the paradox is). In Europe, haloperidol is still the reference substance used in clinical trials despite the fact that it is not officially indicated in the treatment of mania. In the USA, lithium, divalproate, or antipsychotics can be prescribed as first-line treatment. In Europe, lithium remains the first-line medication, whereas divalproate and atypical antipsychotic agents are used only as second-line therapy. Although both types of medication (antipsychotics, normothymic agents, and/or anticonvulsants) have proved to be clinically effective in the management of mania by reducing the mania scores overall, the same does not apply, however, to all symptoms of mania. Factorial approaches to mania have all shown that since there are several clinical forms of mania, several clusters of manic symptoms can be identified. Antipsychotic and normothymic agents and/or anticonvulsants do not appear to have the same effects on each of these identifiable clusters of symptoms, mainly psychotic features. We believe that it is vitally important for future clinical trials of mania treatment to focus on the treatment effect by adopting a factorial approach to characterization of the episode using an appropriate methodological structure. These questions highlight the uncertainty shrouding the very structure of manic episodes, namely that these are predominantly of a thymic or psychotic nature. The Europeans undoubtedly consider mania to be more of a thymic episode and prefer lithium as the first-line treatment, whereas the Americans believe that psychotic symptoms dominate and widely prescribe antipsychotic agents. However, from the standpoint of clinical trials currently available, even though antipsychotic agents are certainly effective in reducing the scores on the mania scales, it is not clear whether they can be considered purely as antimania treatments.
Navigating Imprecision in Relevance Assessments on the Road to Total Recall: Roger and Me

Technology-assisted review ("TAR") systems seek to achieve "total recall"; that is, to approach, as nearly as possible, the ideal of 100% recall and 100% precision, while minimizing human review effort. The literature reports that TAR methods using relevance feedback can achieve considerably greater than the 65% recall and 65% precision reported by Voorhees as the "practical upper bound on retrieval performance. since that is the level at which humans agree with one another" (Variations in Relevance Judgments and the Measurement of Retrieval Effectiveness, 2000). This work argues that in order to build - as well as to, evaluate - TAR systems that approach 100% recall and 100% precision, it is necessary to model human assessment, not as absolute ground truth, but as an indirect indicator of the amorphous property known as "relevance. " The choice of model impacts both the evaluation of system effectiveness, as well as the simulation of relevance feedback. Models are presented that better fit available data than the infallible ground-truth model. These models suggest ways to improve TAR-system effectiveness so that hybrid human-computer systems can improve on both the accuracy and efficiency of human review alone. This hypothesis is tested by simulating TAR using two datasets: the TREC 4 AdHoc collection, and a dataset consisting of 401,960 email messages that were manually reviewed and classified by a single individual, Roger, in his official capacity as Senior State Records Archivist. The results using the TREC 4 data show that TAR achieves higher recall and higher precision than the assessments by either of two independent NIST assessors, and blind adjudication of the email dataset, conducted by Roger, more than two years after his original review, shows that he could have achieved the same recall and better precision, while reviewing substantially fewer than 401,960 emails, had he employed TAR in place of exhaustive manual review.
HSP47 Increases the Expression of Type I Collagen in Fibroblasts through IRE1α Activation, XBP1 Splicing, and Nuclear Translocation of β-Catenin

Heat shock protein 47 (HSP47), also known as SERPINH1, functions as a collagen-specific molecular chaperone protein essential for the formation and stabilization of the collagen triple helix. Here, we delved into the regulatory pathways governed by HSP47, shedding light on collagen homeostasis. Our investigation revealed a significant reduction in HSP47 mRNA levels in the skin tissue of older mice as compared to their younger counterparts. The augmented expression of HSP47 employing lentivirus infection in fibroblasts resulted in an increased secretion of type I collagen. Intriguingly, the elevated expression of HSP47 in fibroblasts correlated with increased protein and mRNA levels of type I collagen. The exposure of fibroblasts to IRE1α RNase inhibitors resulted in the reduced manifestation of HSP47-induced type I collagen secretion and expression. Notably, HSP47-overexpressing fibroblasts exhibited increased XBP1 mRNA splicing. The overexpression of HSP47 or spliced XBP1 facilitated the nuclear translocation of β-catenin and transactivated a reporter harboring TCF binding sites on the promoter. Furthermore, the overexpression of HSP47 or spliced XBP1 or the augmentation of nuclear β-catenin through Wnt3a induced the expression of type I collagen. Our findings substantiate that HSP47 enhances type I collagen expression and secretion in fibroblasts by orchestrating a mechanism that involves an increase in nuclear β-catenin through IRE1α activation and XBP1 splicing. This study therefore presents potential avenues for an anti-skin-aging strategy targeting HSP47-mediated processes.
Circuit resistance training in persons with complete paraplegia.

BACKGROUND/OBJECTIVE We assessed the metabolic and heart rate (HR) responses to a single session of circuit resistance training (CRT) in six subjects with complete paraplegia (T5-T12 levels) in order to determine the caloric cost of the exercise. METHODS Subjects underwent isoinertial weight training exercises with interspersed periods of high-cadence, low-resistance arm ergometry (AE). Following protocol familiarization, subjects completed one session of CRT during which continuous monitoring of HR, oxygen uptake (VO2), and respiratory exchange ratio (RER = VCO2/VO2) was performed. Caloric cost was calculated from the exercise VO2 values across the CRT session. A peak arm exercise test allowed data to be expressed as percentages of peak VO2 and HR. RESULTS Subjects displayed mean VO2 values of 11.6 +/- 2.4 ml/kg/min (mean +/- SD) and a mean HR of 136 +/- 17 beats/min across the CRT session, corresponding with 49.0% of peak VO2 and 76.8% of peak HR. The RER values ranged from 0.96 to 1.19 and averaged above unity throughout the CRT session. CONCLUSION Despite the modest absolute VO2 during exercise, CRT satisfies operational criteria developed for cardiorespiratory exercise prescriptions in persons without disability. The RER values recorded indicate that CRT is intense work that relies primarily on glycolytic metabolism.
Ticlopidine and clopidogrel, sometimes combined with aspirin, only minimally increase the surgical risk in renal transplantation: a case-control study.

BACKGROUND Patients undergoing kidney transplantation are sometimes being treated with antiplatelet agents such as ticlopidine or clopidogrel. Some teams refuse to wait-list these patients for fear of bleeding during transplant surgery. METHODS We retrospectively reviewed the records of 702 adult patients with a kidney transplant alone between 2000 and 2010. Nineteen (2.7%) patients were taking clopidogrel or ticlopidine when called in for transplantation. Furthermore, 10 of these 19 patients were also taking low-dose aspirin (ASA). We compared the risk of bleeding peri- and postoperatively, and the occurrence of cardiovascular complications within 30 days after renal transplantation between 19 cases and 39 controls randomly selected within the cohort. RESULTS Platelets were administered to 7 cases (37%) versus 0 controls (P<0.001). A single case (5.3%) presented with significant bleeding during surgery following an implantation biopsy, and required 4 red bood cell (RBC) units. During the first day, 3 of the 19 cases (16%) and 1 of the 39 controls required RBC (P=0.1). No reoperation was performed for bleeding. After the transplant, clopidogrel or ticlopidine was resumed in only two patients. The platelet count and haemoglobin were similar between cases and controls at Day 30. No cardiovascular event occurred in cases or controls during the first month post-transplantation. At 5 years, graft and patient survival was similar in cases and controls. CONCLUSIONS Clopidogrel and ticlopidine, sometimes in combination with ASA, are associated with a low risk of bleeding during renal transplantation and does not seem to be a contraindication for renal transplant surgery.
Networks of Parvalbumin-Positive Interneurons in the Basolateral Amygdala

The amygdala is a temporal lobe structure that is required for processing emotional information. Polymodal sensory information enters the amygdala at the level of the basolateral amygdala (BLA) and undergoes local processing, after which the behavioral and autonomic responses that accompany emotions are initiated. Two main neuron types are present in the BLA, pyramidal-like principal neurons that use glutamate as their transmitter, and local circuit interneurons that use GABA as their transmitter. Although the properties of principal neurons are known in some detail, very little is known about the properties of BLA interneurons or the local circuits in which they are involved. Using mice in which EGFP (enhanced green fluorescent protein) is expressed under the control of the parvalbumin promoter, we characterized the properties of parvalbumin-positive interneurons in the BLA. By making recordings from interneuron–interneuron and interneuron–principal neuron pairs, we analyzed the intrinsic circuitry of the BLA. We show that parvalbumin-positive interneurons can be divided into four subtypes as defined by their firing properties. Interneurons are electrically coupled in subtype-specific networks and exhibit subtype-specific heterogeneities in their synaptic dynamics and patterns of connectivity. We propose that these properties allow networks of parvalbumin-expressing neurons to perform an array of information-processing tasks within the BLA.
Effects of Age, Sex, and Brightness of Field on Open-Field Behaviors of Rats

48 male and 48 female Holtzman rats, ages 50, 100, and 150 days, were tested in a black or white open field to determine the effect of varying brightness of the field upon ambulation and defecation scores. There were significant negative correlations between all ambulation and defecation scores, except for the 50-day-old animals. Ambulation scores decreased over trials for all animals; defecation scores remained the same. Trials did not interact with age, sex, or brightness on either measure. In both fields females crossed more squares than males at ages 100 and 150 days, but there were no sex differences in ambulation at age 50 days. Most notable was a sex difference as a function of brightness of field; whereas male scores did not differ, females ambulated significantly more and tended to defecate less in the white field. Results are described in terms of the need for standardization of the open field.
Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.
Prenatal programming of hypernatremia and hypertension in neonatal lambs.

Maternal water restriction and the accompanying dehydration-induced anorexia may induce long-term physiological changes in offspring. We determined the impact of prenatal hypertonicity (Pre-Dehy) on offspring cardiovascular and osmoregulatory function. Pre-Dehy lambs were exposed to in utero hypernatremia (8- to 10-meq increase; 110-150 days of gestation) induced by maternal water restriction. Control lambs were born to ewes provided ad libitum water and food throughout gestation. After delivery, all ewes were provided ad libitum water and all newborns were allowed ad libitum nursing. Lambs were prepared with vascular and bladder catheters at 15 +/- 2 days of age and studied at 21 +/- 2 days. After a 2-h basal period, lambs received an infusion of hypotonic (0.075 M) NaCl (0.15 ml.kg(-1). h(-1) iv) for 2 h. Lamb arterial blood pressure was monitored, and blood samples were obtained before, during, and after infusion. During the neonatal basal period, Pre-Dehy lambs had significantly increased plasma osmolality (302 +/- 1 vs. 294 +/- 1 mosmol/kgH(2)O, P < 0.01), sodium levels (144 +/- 1 vs. 140 +/- 1 meq/l, P < 0.01), hematocrit (28 +/- 1% vs. 25 +/- 1%, P < 0.05), and mean arterial blood pressure (79 +/- 2 vs. 68 +/- 1 mmHg, P < 0.001) compared with control lambs. Despite the infusion of hypotonic saline, Pre-Dehy lambs maintained relative hypertonicity, hypernatremia, and hypertension. However, plasma arginine vasopressin, glomerular filtration rate, and urinary osmolar and sodium excretion and clearance (per kg body wt) were similar in the groups. Offspring of prenatally water-restricted ewes exhibit hypernatremia, hypertonicity, and hypertension, which persist despite hypotonic saline infusion. In utero hypertonicity and perhaps maternal nutrient stress may program offspring osmoregulation and systemic arterial hypertension.
Analysis and non-linear control of SEPIC dc-dc converter in photovoltaic systems

SEPIC dc-dc converter has multiple applications as a power conditioning system because it has a non-pulsating input current and its voltage ratio is both step-down and step-up. However, due to the non-linear characteristics of a SEPIC converter, a non-linear control is more suitable to attain better performance in voltage regulation. We designed a Sliding-Mode control and a passivity-based control for controlling both the output voltage of the SEPIC converter and the input voltage to reach the maximum power of a photovoltaic module. This paper presents the stability analysis and the design of the two non-linear controllers. The simulation results show a good performance of both controllers with fast transient responses and zero steady errors. However, the Sliding-Mode control shows less inductor current than the Passivity-Based control. These results confirm the good performance of non-linear control for a SEPIC converter in photovoltaic systems; we expect experimental validations in future work.
Effects of Integrating Therapeutic Touch into a Cognitive Behavioral Pain Treatment Program

The purpose of this study was to investigate the effects of offering Therapeutic Touch (TT) as an adjunct to cognitive behavioral therapy (CBT) for people with chronic pain. Patients were randomized to relaxation training (control group) or TT plus relaxation (experimental). Subsequently, all participants attended a CBT program. Preprogram and postprogram data were examined to identify patterns of change in pain intensity, self-efficacy, unitary power, disability, and perceived distress. In addition, patterns of attrition were examined. Patients in this study who were randomized to receive TT fared better in terms of enhanced self-efficacy and unitary power, as well as having lower attrition rates. Trends associated TT with less distress and disability. This pilot study suggests that offering TT as an adjunct to CBT may help to improve clinical outcomes, reduce program attrition, and promote unitary power in those who suffer with chronic pain.