Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a new exon 2-skipped TNFR1 transcript: regulation by three functional polymorphisms of the TNFR-associated periodic syndrome (TRAPS) gene

Background Mutations in the TNFRSF1A gene encoding the tumour necrosis factor α cell surface receptor, TNFR1, cause TNFR-associated periodic syndrome (TRAPS) and polymorphisms in TNFRSF1A, including rs4149570, rs767455 and rs1800692, are associated with inflammatory diseases. Objectives To describe a new exon 2-spliced transcript—TNFR1-d2—and the impact of these three single nucleotide polymorphisms on exon 2 splicing, transcriptional activity of TNFRSF1A and TRAPS phenotype. Methods Expression of TNFRSF1A transcripts was performed by reverse-transcription-PCR in a range of human cells and tissues. Exon 2 splicing and transcriptional activity were analysed in HEK293T and SW480 cells by in vitro alternative splicing and luciferase assays, respectively. We constructed haplotypes containing rs4149570, rs767455 and rs1800692 in controls (n=72), patients with TRAPS (n=111) and in TRAPS-like patients (n=450) to compare their distribution and association with clinical features of TRAPS. Results TNFR1-d2 was expressed in a tissue-specific manner, whereas TNFR1 expression was ubiquitous. Alternative splicing assays showed that the T-A-T haplotype at rs4149570–rs767455–rs1800692 had a significantly higher expression of exon 2-skipping product (p=0.02) compared with the G-G-C haplotype. Transcriptional activity from the T-T haplotype at rs4149570–rs1800692 was increased compared with the G-C haplotype (p=0.03). In patients with TRAPS, rs1800692 T/T homozygotes were excessively rare (p<10−4) and TRAPS-like patients with this genotype experienced less fever. Conclusions Our study provides a new mechanism of TNFRSF1A regulation whereby three polymorphisms in the promoter, exon 1 and intron 4 have a functional and combined effect on exon 2 splicing, via a coupling mechanism between transcription and splicing. These polymorphisms may affect the phenotype of TRAPS and TRAPS-like patients.
OLAP textual aggregation approach using the Google similarity distance

Data warehousing and online analytical processing OLAP are essential elements to decision support. In the case of textual data, decision support requires new tools, mainly textual aggregation functions, for better and faster high level analysis and decision making. Such tools will provide textual measures to users who wish to analyse documents online. In this paper, we propose a new aggregation function for textual data in an OLAP context based on the K-means method. This approach will highlight aggregates semantically richer than those provided by classical OLAP operators. The distance used in K-means is replaced by the Google similarity distance which takes into account the semantic similarity of keywords for their aggregation. The performance of our approach is analysed and compared to other methods such as Topkeywords, TOPIC, TuBE and BienCube. The experimental study shows that our approach achieves better performances in terms of recall, precision, F-measure complexity and runtime.
Annulus amplitudes and ZZ branes in minimal string theory

We study the annulus amplitudes of (p,q) minimal string theory. Focusing on the ZZ-FZZT annulus amplitude as a target-space probe of the ZZ brane, we use it to confirm that the ZZ branes are localized in the strong-coupling region. Along the way we learn that the ZZ-FZZT open strings are fermions, even though our theory is bosonic! We also provide a geometrical interpretation of the annulus amplitudes in terms of the Riemann surface p,q that emerges from the FZZT branes. The ZZ-FZZT annulus amplitude measures the deformation of p,q due to the presence of background ZZ branes; each kind of ZZ-brane deforms only one A-period of the surface. Finally, we use the annulus amplitudes to argue that the ZZ branes can be regarded as ``wrong-branch tachyons which violate the bound α
Survey of local algorithms

A local algorithm is a distributed algorithm that runs in constant time, independently of the size of the network. Being highly scalable and fault tolerant, such algorithms are ideal in the operation of large-scale distributed systems. Furthermore, even though the model of local algorithms is very limited, in recent years we have seen many positive results for nontrivial problems. This work surveys the state-of-the-art in the field, covering impossibility results, deterministic local algorithms, randomized local algorithms, and local algorithms for geometric graphs.
Predicting Diabetic Nephropathy Using a Multifactorial Genetic Model

Aims The tendency to develop diabetic nephropathy is, in part, genetically determined, however this genetic risk is largely undefined. In this proof-of-concept study, we tested the hypothesis that combined analysis of multiple genetic variants can improve prediction. Methods Based on previous reports, we selected 27 SNPs in 15 genes from metabolic pathways involved in the pathogenesis of diabetic nephropathy and genotyped them in 1274 Ashkenazi or Sephardic Jewish patients with Type 1 or Type 2 diabetes of >10 years duration. A logistic regression model was built using a backward selection algorithm and SNPs nominally associated with nephropathy in our population. The model was validated by using random “training” (75%) and “test” (25%) subgroups of the original population and by applying the model to an independent dataset of 848 Ashkenazi patients. Results The logistic model based on 5 SNPs in 5 genes (HSPG2, NOS3, ADIPOR2, AGER, and CCL5) and 5 conventional variables (age, sex, ethnicity, diabetes type and duration), and allowing for all possible two-way interactions, predicted nephropathy in our initial population (C-statistic = 0.672) better than a model based on conventional variables only (C = 0.569). In the independent replication dataset, although the C-statistic of the genetic model decreased (0.576), it remained highly associated with diabetic nephropathy (χ2 = 17.79, p<0.0001). In the replication dataset, the model based on conventional variables only was not associated with nephropathy (χ2 = 3.2673, p = 0.07). Conclusion In this proof-of-concept study, we developed and validated a genetic model in the Ashkenazi/Sephardic population predicting nephropathy more effectively than a similarly constructed non-genetic model. Further testing is required to determine if this modeling approach, using an optimally selected panel of genetic markers, can provide clinically useful prediction and if generic models can be developed for use across multiple ethnic groups or if population-specific models are required.
A unified approach of incorporating general features in decision tree based acoustic modeling

A unified maximum likelihood framework of incorporating phonetic and non-phonetic features in decision tree based acoustic modeling is proposed. Unlike phonetic features, non-phonetic features in this context are those features, which cannot be derived from the phoneme identities. Although non-phonetic features are used in speech recognition, they are often treated separately and based on various heuristics. In our approach, non-phonetic features are included as additional tags to the decision tree clustering. Moreover, the proposed tagged decision tree is based on the full training data, and therefore, it alleviates the problem of training data depletion in building specific feature dependent acoustic models. Experimental results indicate that up to 10% word error rate reduction can be achieved in a large vocabulary (Wall Street Journal) speech recognition task based on the proposed approach.
Risk factors for poor bone health in adolescents and adults with CHARGE syndrome

CHARGE syndrome, is associated with genital hypoplasia, feeding difficulties and delayed puberty. In this study we examined the prevalence of risk factors for poor bone health in adolescents and adults with CHARGE. Questionnaires assessing fracture history, dietary intake of calcium and vitamin D, pubertal status and activity level using the Habitual Activity Estimation Scale (HAES) were completed by caregivers. Control data were collected for the HAES. When available, reports from dual‐energy X‐ray absorptiometry (DEXA) were obtained. Thirty individuals with CHARGE syndrome (n = 15 males; n = 15 females; age range 13 to 34 years; mean age 19.6 years) were recruited. Traumatic bony fractures were identified in 30% of the population. The recommended nutritional intake (RNI) for calcium and vitamin D were not met by 41% and 87% of the population, respectively, and 53% required past tube feeding. Delayed puberty was experienced by 87% with only 4 individuals (2 female, 2 males) having experienced normal puberty. Hormone replacement therapy (HRT) was taken by 33% of females and 60% of males. According to the HAES, adolescents with CHARGE syndrome (13–18 years) were significantly less active than controls. Individuals with CHARGE syndrome age 19 and older were also less active than controls, although this difference was not significant. DEXA scan data was obtained, however, due to small sample size (n = 10) and confounding variables (i.e., short stature, pubertal stage, height, weight), it was difficult to draw meaningful conclusions. Feeding difficulties, inactivity and hypogonadism are predisposing factors for the development of poor bone health among individuals with CHARGE syndrome. Education is necessary to raise awareness regarding the importance of HRT, proper nutrition and weight‐bearing activity for healthy bone development and maintenance in individuals with CHARGE syndrome. © 2007 Wiley‐Liss, Inc.
Role of P120 Ras-Gap in Directed Cell Movement

We have used cell lines deficient in p120 Ras GTPase activating protein (Ras-GAP) to investigate the roles of Ras-GAP and the associated p190 Rho-GAP (p190) in cell polarity and cell migration. Cell wounding assays showed that Ras-GAP–deficient cells were incapable of establishing complete cell polarity and migration into the wound. Stimulation of mutant cells with growth factor rescued defects in cell spreading, Golgi apparatus fragmentation, and polarized vesicular transport and partially rescued migration in a Ras-dependent manner. However, for directional movement, the turnover of stress fibers and focal adhesions to produce an elongate morphology was dependent on the constitutive association between Ras-GAP and p190, independent of Ras regulation. Disruption of the phosphotyrosine-mediated Ras-GAP/p190 complex by microinjecting synthetic peptides derived from p190 sequences in wild-type cells caused a suppression of actin filament reorientation and migration. From these observations we suggest that although Ras-GAP is not directly required for motility per se, it is important for cell polarization by regulating actin stress fiber and focal adhesion reorientation when complexed with 190. This observation suggests a specific function for Ras-GAP separate from Ras regulation in cell motility.
Complex-network theoretic clustering for identifying groups of similar listeners in p2p systems

This article presents an approach to automatically create virtual communities of users with similar music preferences in a distributed system. Our goal is to create personalized music channels for these communities using the content shared by its members in peer-to-peer networks for each community. To extract these communities a complex network theoretic approach is chosen. A fully connected graph of users is created using epidemic protocols. We show that the created graph sufficiently converges to a graph created with a centralized algorithm after a small number of protocol iterations. To find suitable techniques for creating user communities, we analyze graphs created from real-world recommender datasets and identify specific properties of these datasets. Based on these properties, different graph-based community-extraction techniques are chosen and evaluated. We select a technique that exploits identified properties to create clusters of music listeners. The suitability of this technique is validated using a music dataset and two large movie datasets. On a graph of 6,040 peers, the selected technique assigns at least 85% of the peers to optimal communities, and obtains a mean classification error of less than 0.05% over the remaining peers that are not assigned to the best community.
Sex differences in tendon structure and function

Tendons play a critical role in the transmission of forces between muscles and bones, and chronic tendon injuries and diseases are among the leading causes of musculoskeletal disability. Little is known about sex‐based differences in tendon structure and function. Our objective was to evaluate the mechanical properties, biochemical composition, transcriptome, and cellular activity of plantarflexor tendons from 4 month old male and female C57BL/6 mice using in vitro biomechanics, mass spectrometry‐based proteomics, genome‐wide expression profiling, and cell culture techniques. While the Achilles tendons of male mice were approximately 6% larger than female mice (p < 0.05), the cell density of female mice was around 19% greater than males (p < 0.05). No significant differences in mechanical properties (p > 0.05) of plantaris tendons were observed. Mass spectrometry proteomics analysis revealed no significant difference between sexes in the abundance of major extracellular matrix (ECM) proteins such as collagen types I (p = 0.30) and III (p = 0.68), but female mice had approximately twofold elevations (p < 0.05) in less abundant ECM proteins such as fibronectin, periostin, and tenascin C. The transcriptome of male and female tendons differed by only 1%. In vitro, neither the sex of the serum that fibroblasts were cultured in, nor the sex of the ECM in which they were embedded, had profound effects on the expression of collagen and cell proliferation genes. Our results indicate that while male mice expectedly had larger tendons, male and female tendons have very similar mechanical properties and biochemical composition, with small increases in some ECM proteins and proteoglycans evident in female tendons. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2117–2126, 2017.
Characterization of the Genome Composition of Bartonella koehlerae by Microarray Comparative Genomic Hybridization Profiling

ABSTRACT Bartonella henselae is present in a wide range of wild and domestic feline hosts and causes cat-scratch disease and bacillary angiomatosis in humans. We have estimated here the gene content of Bartonella koehlerae, a novel species isolated from cats that was recently identified as an agent of human endocarditis. The investigation was accomplished by comparative genomic hybridization (CGH) to a microarray constructed from the sequenced 1.93-Mb genome of B. henselae. Control hybridizations of labeled DNA from the human pathogen Bartonella quintana with a reduced genome of 1.58 Mb were performed to evaluate the accuracy of the array for genes with known levels of sequence divergence. Genome size estimates of B. koehlerae by pulsed-field gel electrophoresis matched that calculated by the CGH, indicating a genome of 1.7 to 1.8 Mb with few unique genes. As in B. quintana, sequences in the prophage and the genomic islands were reported absent in B. koehlerae. In addition, sequence variability was recorded in the chromosome II-like region, where B. koehlerae showed an intermediate retention pattern of both coding and noncoding sequences. Although most of the genes missing in B. koehlerae are also absent from B. quintana, its phylogenetic placement near B. henselae suggests independent deletion events, indicating that host specificity is not solely attributed to genes in the genomic islands. Rather, the results underscore the instability of the genomic islands even within bacterial populations adapted to the same host-vector system, as in the case of B. henselae and B. koehlerae.
Agonist-induced isotonic contraction of cultured mesangial cells after multiple passage.

Contractile cells under conditions of prolonged culture lose their ability to contract in the usual manner (i.e., isotonically). One explanation for this may be that contraction is prevented by tight cell-to-substrate adhesion. Two models in which substrate adhesiveness was expected to be diminished were used to test this hypothesis. In one, cells were seeded onto collagen-coated dishes and used within 40 min of plating. In the other, cells were plated onto dishes coated with poly-2-hydroxyethyl methacrylate (poly-HEMA) and used, depending on thickness of the poly-HEMA substrate, up to periods of 1 wk. Cells plated onto such substrates contracted when challenged with either PGE2 (2 X 10(-6) and 2 X 10(-9) M), arginine vasopressin (AVP, 10(-6)-10(-9) ), or the calcium ionophore A23187 (5 micrograms/ml). Contraction took place within 5-15 min at 37 degrees C. The contraction seen with AVP was due to its pressor action because 1-desamino-8-D-arginine vasopressin (dDAVP), the antidiuretic analogue, did not cause contraction and the anti-pressor analogue [1-(beta-mercapto-beta beta-cyclopentamethylene propionic acid)-4-valine 8-D-arginine]-vasopressin [d(CH2)5-VDAVP] blocked contraction by AVP. The contraction seen with AVP was dependent on extracellular calcium, whereas that observed with prostaglandin E2 (PGE2) was not. (ABSTRACT TRUNCATED AT 250 WORDS)
Temporal trends of neuro-autonomic complexity during severe episodes of bipolar disorders

Bipolar disorder is a chronic psychiatric condition during which patients experience mood swings among depression, hypomania or mania, mixed state (depression-hypomania) and euthymia, i.e., good affective balance. Nowadays, an objective characterization of the temporal trends of the disease as a response to the pharmacological treatment through physiological signatures, especially during severe episodes, is still missing. In this study we show interesting findings relating neuro-autonomic complexity to severe pathological mood states. More specifically, we studied Sample Entropy (SampEn) measures on Heart Rate Variability series gathered from four bipolar patients recruited within the frame of the European project PSYCHE. Patients were monitored through long term ECG recordings from the first hospital admission until clinical remission, i.e., the euthymic state. We observed that a mood transition from mixed-state to euthymia passing through depression can be characterized by increased SampEn values, i.e. as the patient is going to recover, SampEn increases. These results are in agreement with the current literature reporting on the complexity dynamics of the cardiovascular system and can provide a promising and viable clinical decision support to objectify the diagnosis and improve the management of psychiatric disorders.
Semantic Speech Tagging: Towards Combined Analysis of Speaker Traits

A number of paralinguistic problems are often dealt with in isolation, such as emotion, health state or personality. However, there are also good examples of mutual benefit, mostly incorporating speaker gender knowledge. In this paper we deal with the question how further paralinguistic information, such as speaker age, height, or race can provide beneficial information when their ground truth knowledge is provided within single-task speaker classification. Tests with openSMILE’s 1.5 k Paralinguistic Challenge Feature set on the TIMIT corpus of 630 speakers reveal significant boost in accuracy or cross-correlation—depending on the representation form of the problem at hand.
Bilinear Factor Analysis for iVector Based Speaker Verification

The combination of iVector extraction and Probabilistic Linear Discriminant Analysis (PLDA) model forms a basis of the current state of the art speaker veriﬁcation. The PLDA model makes an assumption that the within-speaker (or inter-session) variability in the iVector space is independent of speaker identity. In this work we propose a new model, which can be seen as an extension of PLDA, relaxing this assumption and allow-ing the within-speaker variability to be different for different locations of speakers in the iVector space. The potential of the proposed model is demonstrated in preliminary experiments. in iVector independent identity.
Orthostatic Changes in Hemodynamics and Cardiovascular Biomarkers in Dysautonomic Patients

Background Impaired autonomic control of postural homeostasis results in orthostatic intolerance. However, the role of neurohormones in orthostatic intolerance has not been explained. Methods Six-hundred-and-seventy-one patients (299 males; 55±22 years) with unexplained syncope underwent head-up tilt (HUT) with serial blood sampling. Systolic blood pressure (SBP) and heart rate (HR) supine, after 3min, and lowest BP/highest HR during HUT were recorded. Plasma levels of epinephrine, norepinephrine, renin, C-terminal-pro-arginine-vasopressin (CT-proAVP), C-terminal- endothelin-1 (CT-proET-1), and mid-regional-fragment of pro-atrial-natriuretic-peptide (MR-proANP) were determined at supine and 3min of HUT. Multivariate-adjusted logistic regression model was applied to compare 1st (reference) with 4th quartile of 3 min and maximal ΔSBP/ΔHR (i.e. pronounced hypotension or tachycardia) vs. changes in neuroendocrine biomarkers, respectively. Results Higher resting CT-proET-1 predicted BP fall at 3min (Odds ratio (OR) per 1 SD: 1.62, 95%CI 1.18–2.22; p = 0.003), and max BP fall during HUT (1.82, 1.28–2.61; p = 0.001). Higher resting CT-proAVP predicted BP fall at 3min (1.33, 1.03–1.73; p = 0.03), which was also associated with increase in CT-proAVP (1.86, 1.38–2.51; p = 0.00005) and epinephrine (1.47, 1.12–1.92; p = 0.05) during HUT. Lower resting MR-proANP predicted tachycardia at 3min (0.37, 0.24–0.59; p = 0.00003), and max tachycardia during HUT (0.47, 0.29–0.77; p = 0.002). Further, tachycardia during HUT was associated with increase in epinephrine (1.60, 1.15–2.21; p = 0.005), and norepinephrine (1.87, 1.38–2.53; p = 0.005). Conclusions Resting CT-proET-1 and CT-proAVP are increased in orthostatic hypotension, while resting MR-proANP is decreased in postural tachycardia. Moreover, early BP fall during orthostasis evokes increase in CT-proAVP and epinephrine, while postural tachycardia is associated with increase in norepinephrine and epinephrine.
High Grade Penetrating Pancreatic Trauma - Case Report and Review of the Literature.

INTRODUCTION The pancreatic injuries have fortunately a low frequency, but when present associate multiple intraabdominal lesions, and carry a significant morbidity and mortality. The aim of this study is to underline the significant morbidity associated with high grade pancreatic injuries. CASE REPORT Female patient, 36 years old, with penetrating abdominal trauma due to domestic violence was referred to our center from a regional county hospital, after multiple laparotomies, hemodynamically unstable, with multiple organ failure. Abdominal clinical exam revealed evisceration, with massive pancreatic leakage at the level of the median laparotomy and through the stabbing wounds from the right flank. Emergency Computed Tomography showed multiple intraabdominal collections, with laceration of the liver, right kidney and pancreatic head. Abdominal exploration was decided. After a thorough abdominal debridement was revealed a deep laceration of the pancreatic head, with active extravasation of pancreatic secretion, correlating with a grade IV injury. Peritoneal lavage and large drainage of the lesser and greater peritoneal cavity was performed. The postoperative recovery was uneventful, with progressive decrease in pancreatic fistula output and discharge after 35 days. CONCLUSIONS High grade pancreatic traumas associate a significant morbidity. Efficient drainage of the pancreatic head injuries and patients management in high volume centers for pancreatic surgery maximize the survival rate.