Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross language information retrieval in Twenty One Using one some or all possible translations

This paper gives an overview of the tools and methods for Cross Language Information Re trieval CLIR that were developed within the Twenty One project The tools and methods are evaluated with the TREC CLIR task document collection using Dutch queries on the English doc ument base The main issue addressed here is an evaluation of two approaches to disambiguation The underlying question is whether a lot of e ort should be put in nding the correct translation for each query term before searching or whether searching with more than one possible transla tion leads to better results The experimental study suggests that in terms of average preci sion searching with ambiguities leads to better retrieval performance than searching with disam biguated queries
Cardiospecific microRNA Plasma Levels Correlate with Troponin and Cardiac Function in Patients with ST Elevation Myocardial Infarction, Are Selectively Dependent on Renal Elimination, and Can Be Detected in Urine Samples

Objectives: Circulating microRNAs (miRNAs) are promising as biomarkers for various diseases. We examined the release patterns of cardiospecific miRNAs in a closed-chest, large animal ischemia-reperfusion model and in patients with ST elevation myocardial infarction (STEMI). Methods: Six anesthetized pigs were subjected to coronary occlusion-reperfusion. Plasma, urine, and clinical parameters were collected from 25 STEMI patients undergoing primary percutaneous coronary intervention. miRNA was extracted and measured with qPCR. Results: In the pig reperfusion model miR-1, miR-133a, and miR-208b increased rapidly in plasma with a peak at 120 min, while miR-499-5p remained elevated longer. In patients with STEMI all 4 miRNAs increased abruptly from 70-fold to 3,000-fold in plasma, with a peak within 12 h (p < 0.01). miR-1 and miR-133a both correlated strongly with the glomerular filtration rate (GFR), indicating renal elimination. This was confirmed by detection of miR-1 and miR-133a, but not miR-208b or miR-499-5p, in urine. Peak values of miR-208b correlated with peak troponin and the ejection fraction. Conclusion: We demonstrate a distinct and rapid increase in levels of cardiospecific miRNA in the circulation after myocardial infarction. Release of miRNAs correlated with cardiomyocyte necrosis markers, the ejection fraction, and the GFR, indicating a possible role for these molecules as biomarkers for the diagnosis of STEMI as well as the prediction of long-term complications.
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free energies for macromolecules by combining molecular mechanics calculations and continuum solvation models. To systematically evaluate the performance of these methods, we report here an extensive study of 59 ligands interacting with six different proteins. First, we explored the effects of the length of the molecular dynamics (MD) simulation, ranging from 400 to 4800 ps, and the solute dielectric constant (1, 2, or 4) on the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1) MD simulation length has an obvious impact on the predictions, and longer MD simulation is not always necessary to achieve better predictions. (2) The predictions are quite sensitive to the solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/ligand binding interface. (3) Conformational entropy often show large fluctuations in MD trajectories, and a large number of snapshots are necessary to achieve stable predictions. Next, we evaluated the accuracy of the binding free energies calculated by three Generalized Born (GB) models. We found that the GB model developed by Onufriev and Case was the most successful model in ranking the binding affinities of the studied inhibitors. Finally, we evaluated the performance of MM/GBSA and MM/PBSA in predicting binding free energies. Our results showed that MM/PBSA performed better in calculating absolute, but not necessarily relative, binding free energies than MM/GBSA. Considering its computational efficiency, MM/GBSA can serve as a powerful tool in drug design, where correct ranking of inhibitors is often emphasized.
Expansion and contraction of the hepatitis B virus transcriptional template in infected chimpanzees

We have previously shown that hepatitis B virus (HBV) replication is controlled by noncytolytic mechanisms that depend primarily on the effector functions of the CD8+ T cell response, especially the production of IFN-γ in the liver. The mechanisms that control the nuclear pool of viral covalently closed circular DNA (cccDNA) transcriptional template of HBV, which must be eliminated to eradicate infection, have been difficult to resolve. To examine those mechanisms, we quantitated intrahepatic HBV cccDNA levels in acutely infected chimpanzees whose virological, immunological, and pathological features were previously described. Our results demonstrate that the elimination kinetics of the cccDNA are more rapid than the elimination of HBV antigen-positive hepatocytes during the early phase of viral clearance, and they coincide with the influx of small numbers of IFN-γ producing CD8+ T cells into the liver. In contrast, terminal clearance of the cccDNA is associated with the peak of liver disease and hepatocellular turnover and with a surge of IFN-γ producing CD8+ T cells in the liver. Collectively, these results suggest that cccDNA clearance is a two-step process mediated by the cellular immune response. The first step reduces the pool of cccDNA molecules noncytolytically, probably by eliminating their relaxed circular DNA precursors and perhaps by destabilizing them. The second step enhances this process by destroying infected hepatocytes and triggering their turnover. Surprisingly, despite this multipronged response, traces of cccDNA persist indefinitely in the liver, likely providing a continuous antigenic stimulus that confers lifelong immunity.
Long-Term Course to Lumbar Disc Resorption Patients and Predictive Factors Associated with Disc Resorption

The long-term course to lumbar intervertebral disc herniation (LDH) patients receiving integrative Korean medicine treatment and predictive factors associated with disc resorption were investigated. LDH patients who received integrative Korean medicine treatment from February 2012 to December 2015 and were registered in the “longitudinal project for LDH on MRI” were included. Disc resorption amount was measured 3-dimensionally with disc degeneration and modic change levels on baseline and follow-up MRIs. Patient characteristics, Korean medicine use, pain, symptom recurrence, and satisfaction were assessed through medical records and phone surveys. Of 505 participants, 19 did not show disc resorption, while 486 did. A total of 220 displayed resorption rates of ≥50%. LDH volume at baseline was 1399.82 ± 594.96 mm3, and that on follow-up MRI was 734.37 ± 303.33 mm3, indicating a 47.5% decrease (p < 0.0001). Predictive factors for disc resorption were disc extrusion, Komori migration classification, and LDH amount. Approximately 68.4% did not experience symptom recurrence over the 51.86 ± 19.07-month follow-up, and 90.3% were satisfied with Korean medicine treatment. The majority of LDH patients who improved after integrative Korean medicine treatment showed disc resorption within 1 year with favorable long-term outcomes. Predictive factors for disc resorption should be duly considered for informed decision-making. This trial is registered with ClinicalTrials.gov NCT02841163.
On the decidability and complexity of Metric Temporal Logic over finite words

Metric Temporal Logic (MTL) is a prominent specification formalism for real-time systems. In this paper, we show that the satisfiability problem for MTL over finite timed words is decidable, with non-primitive recursive complexity. We also consider the model-checking problem for MTL: whether all words accepted by a given Alur-Dill timed automaton satisfy a given MTL formula. We show that this problem is decidable over finite words. Over infinite words, we show that model checking the safety fragment of MTL--which includes invariance and time-bounded response properties--is also decidable. These results are quite surprising in that they contradict various claims to the contrary that have appeared in the literature.
Evaluation of Local and Global Features for Offline Signature Verification

In this paper we evaluate the impact of two state- of-the-art offline signature verification systems which are based on local and global features, respectively. It is important to take into account the real world needs of Forensic Handwriting Examiners (FHEs). In forensic scenarios, the FHEs have to make decisions not only about forged and genuine signatures but also about disguised signatures, i.e., signatures where the authentic author deliberately tries to hide his/her identity with the purpose of denial at a later stage. The disguised signatures play an important role in real forensic cases but are usually neglected in recent literaure. This is the novelty of our study and the topic of this paper, i.e., investigating the performance of automated systems on disguised signatures. Two robust offline signature verification systems are slightly improved and evaluated on publicly available data sets from previous signature verification competitions. The ICDAR 2009 offline signature verification competition dataset and the ICFHR 2010 4NSigComp signatures dataset. In our experiments we observed that global features are capable of providing good results if only a detection of genuine and forged signatures is needed. Local features, however, are much better suited to solve the forensic signature verification cases when disguised signatures are also involved. Noteworthy, the system based on local features could outperform all other participants at the ICFHR 4NSigComp 2010. Keywords-signature verification, mixture models, forgeries, disguised signatures, forensic handwriting analysis
Variant allele of HSD3B1 increases progression to castration‐resistant prostate cancer

3β‐hydroxysteroid dehydrogenase type 1 (3βHSD1), which is a rate‐limiting enzyme that catalyzes the conversion of adrenal‐derived steroid dehydroepiandrosterone to dihydrotestosterone (DHT), may be a promising target for treating castration‐resistant prostate cancer (CRPC).
Neuropilin-1-VEGFR-2 Complexing Requires the PDZ-binding Domain of Neuropilin-1*

Vascular endothelial growth factor (VEGF) acts as a hierarchically high switch of the angiogenic cascade by interacting with its high affinity VEGF receptors and with neuropilin co-receptors. VEGF165 binds to both Neuropilin-1 (NP-1) and VEGFR-2, and it is believed that ligand binding forms an extracellular bridge between both molecules. This leads to complex formation, thereby enhancing VEGFR-2 phosphorylation and subsequent signaling. We found that inhibition of VEGF receptor (VEGFR) phosphorylation reduced complex formation between NP-1 and VEGFR-2, suggesting a functional role of the cytoplasmic domain of VEGFR-2 for complex formation. Correspondingly, deleting the PDZ-binding domain of NP-1 decreased complex formation, indicating that extracellular VEGF165 binding is not sufficient for VEGFR-2-NP-1 interaction. Synectin is an NP-1 PDZ-binding domain-interacting molecule. Experiments in Synectin-deficient endothelial cells revealed reduced VEGFR-2-NP-1 complex formation, suggesting a role for Synectin in VEGFR-2-NP-1 signaling. Taken together, the experiments have identified a novel mechanism of NP-1 interaction with VEGFR-2, which involves the cytoplasmic domain of NP-1.
Regularized Iterative Weighted Filtered Back-Projection for Few-View Data Photoacoustic Imaging

Photoacoustic imaging is an emerging noninvasive imaging technique with great potential for a wide range of biomedical imaging applications. However, with few-view data the filtered back-projection method will create streak artifacts. In this study, the regularized iterative weighted filtered back-projection method was applied to our photoacoustic imaging of the optical absorption in phantom from few-view data. This method is based on iterative application of a nonexact 2DFBP. By adding a regularization operation in the iterative loop, the streak artifacts have been reduced to a great extent and the convergence properties of the iterative scheme have been improved. Results of numerical simulations demonstrated that the proposed method was superior to the iterative FBP method in terms of both accuracy and robustness to noise. The quantitative image evaluation studies have shown that the proposed method outperforms conventional iterative methods.
Modular reinforcement learning for self-adaptive energy efficiency optimization in multicore system

Energy-efficiency is becoming increasingly important to modern computing systems with multi-/many-core architectures. Dynamic Voltage and Frequency Scaling (DVFS), as an effective low-power technique, has been widely applied to improve energy-efficiency in commercial multi-core systems. However, due to the large number of cores and growing complexity of emerging applications, it is difficult to efficiently find a globally optimized voltage/frequency assignment at runtime. In order to improve the energy-efficiency for the overall multicore system, we propose an online DVFS control strategy based on core-level Modular Reinforcement Learning (MRL) to adaptively select appropriate operating frequencies for each individual core. Instead of focusing solely on the local core conditions, MRL is able to make comprehensive decisions by considering the running-states of multiple cores without incurring exponential memory cost which is necessary in traditional Monolithic Reinforcement Learning (RL). Experimental results on various realistic applications and different system scales show that the proposed approach improves up to 28% energy-efficiency compared to the recent individual-RL approach.
TFIIH-Associated Cdk7 Kinase Functions in Phosphorylation of C-Terminal Domain Ser7 Residues, Promoter-Proximal Pausing, and Termination by RNA Polymerase II

ABSTRACT The function of human TFIIH-associated Cdk7 in RNA polymerase II (Pol II) transcription and C-terminal domain (CTD) phosphorylation was investigated in analogue-sensitive Cdk7as/as mutant cells where the kinase can be inhibited without disrupting TFIIH. We show that both Cdk7 and Cdk9/PTEFb contribute to phosphorylation of Pol II CTD Ser5 residues on transcribed genes. Cdk7 is also a major kinase of CTD Ser7 on Pol II at the c-fos and U snRNA genes. Furthermore, TFIIH and recombinant Cdk7-CycH-Mat1 as well as recombinant Cdk9-CycT1 phosphorylated CTD Ser7 and Ser5 residues in vitro. Inhibition of Cdk7 in vivo suppressed the amount of Pol II accumulated at 5′ ends on several genes including c-myc, p21, and glyceraldehyde-3-phosphate dehydrogenase genes, indicating reduced promoter-proximal pausing or polymerase “leaking” into the gene. Consistent with a 5′ pausing defect, Cdk7 inhibition reduced recruitment of the negative elongation factor NELF at start sites. A role of Cdk7 in regulating elongation is further suggested by enhanced histone H4 acetylation and diminished histone H4 trimethylation on lysine 36—two marks of elongation—within genes when the kinase was inhibited. Consistent with a new role for TFIIH at 3′ ends, it was detected within genes and 3′-flanking regions, and Cdk7 inhibition delayed pausing and transcription termination.
Shrinkage of ipsilateral taste buds and hyperplasia of contralateral taste buds following chorda tympani nerve transection

The morphological changes that occur in the taste buds after denervation are not well understood in rats, especially in the contralateral tongue epithelium. In this study, we investigated the time course of morphological changes in the taste buds following unilateral nerve transection. The role of the trigeminal component of the lingual nerve in maintaining the structural integrity of the taste buds was also examined. Twenty-four Sprague-Dawley rats were randomly divided into three groups: control, unilateral chorda tympani nerve transection and unilateral chorda tympani nerve transection + lingual nerve transection. Rats were allowed up to 42 days of recovery before being euthanized. The taste buds were visualized using a cytokeratin 8 antibody. Taste bud counts, volumes and taste receptor cell numbers were quantified and compared among groups. No significant difference was detected between the chorda tympani nerve transection and chorda tympani nerve transection + lingual nerve transection groups. Taste bud counts, volumes and taste receptor cell numbers on the ipsilateral side all decreased significantly compared with control. On the contralateral side, the number of taste buds remained unchanged over time, but they were larger, and taste receptor cells were more numerous postoperatively. There was no evidence for a role of the trigeminal branch of the lingual nerve in maintaining the structural integrity of the anterior taste buds.
Can physical activity maintain normal grades of body mass index and body fat percentage?

Background/Aims: A cross-sectional study was undertaken on 767 urban male volunteers performing physical activity and 469 age and socioeconomic status matched controls not doing any physical activity from the city limits of North India. Materials and Methods: Height and weight were recorded for each participant to determine their Body Mass Index (BMI). Body fat percentage and weight was measured using a body fat monitor. Results: Fifty three percent of the physical activity performers showed normal BMI compared to 49% nonphysical activity performers. Overweight was observed in 43.3% physical activity performers compared to 44.7% nonphysical activity performers. Fifty two percent of physical activity performers had normal body fat percent compared to 48.5% nonphysical activity performers. Low body fat percent was observed in 23.4% physical activity performers compared to 2.7% nonphysical activity performers. High body fat percent was observed in 48.7% nonphysical activity performers compared to 45.8% physical activity performers. Conclusions: Overall, the study suggested that physical activity alone cannot maintain BMI and body fat percent, but it can reduce the risk of overweight and high body fat percent in the population.
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance

Basal colonic crypt stem cells are long lived and play a role in colon homeostasis. Previous evidence has shown that high-calorie diet (HCD) enhances colonic stem cell numbers and expansion of the proliferative zone, an important biomarker for colon cancer. However, it is not clear how HCD drives dysregulation of colon stem cell/colonocyte proliferative kinetics. We used a human-relevant pig model and developed an immunofluorescence technique to detect and quantify colonic stem cells. Pigs (n = 8/group) were provided either standard diet (SD; 5% fat) or HCD (23% fat) for 13 weeks. HCD- and SD-consuming pigs had similar total calorie intake, serum iron, insulin, and glucose levels. However, HCD elevated both colonic proliferative zone (KI-67) and stem cell zone (ASCL-2 and BMI-1). Proliferative zone correlated with elevated innate colonic inflammatory markers TLR-4, NF-κB, IL6, and lipocalin-2 (r ≥ 0.62, P = 0.02). Elevated gut bacterial phyla proteobacteria and firmicutes in HCD-consuming pigs correlated with proliferative and stem cell zone. Colonic proteome data revealed the upregulation of proteins involved in cell migration and proliferation and correlated with proliferative and stem cell zone expansion. Our study suggests that pig colon, unlike mice, has two distinct stem cells (ASCL-2 and BMI-1) similar to humans, and HCD increases expansion of colonic proliferative and stem cell zone. Thus, pig model can aid in the development of preventive strategies against gut bacterial dysbiosis and inflammation-promoted diseases, such as colon cancer. Cancer Prev Res; 10(8); 442–50. ©2017 AACR.
A Universal and Stable All-Fiber Refractive Index Sensor System

In this letter, a universal, simple, and stable all-fiber sensor system is proposed to measure the refractive index (RI) of liquids. The basic principle of the technique is based on the relative measurement of the Fresnel reflection from sensor probes. A quadruple of time-division multiplexed Fresnel reflected pulses are obtained from a single nanosecond input pulse owing to the latencies in fibers with different lengths. The measured RIs for the different liquids show that the proposed all-fiber RI sensor system enables linear and repeatable measurements. The performance of the system is compared with the previously published studies, and good agreement is observed, showing the accuracy of the measurements. The standard deviations of the measured RIs are obtained in a short-term measurement as 2.8 × 10-6 for distilled water, and in a long-term measurement as 2.99×10-5 for methanol, showing the high repeatability of the measurements.
Physician-patient communication in the primary care office: a systematic review.

BACKGROUND The physician-patient interview is the key component of all health care, particularly of primary medical care. This review sought to evaluate existing primary-care-based research studies to determine which verbal and nonverbal behaviors on the part of the physician during the medical encounter have been linked in empirical studies with favorable patient outcomes. METHODS We reviewed the literature from 1975 to 2000 for studies of office interactions between primary care physicians and patients that evaluated these interactions empirically using neutral observers who coded observed encounters, videotapes, or audiotapes. Each study was reviewed for the quality of the methods and to find statistically significant relations between specific physician behaviors and patient outcomes. In examining nonverbal behaviors, because of a paucity of clinical outcome studies, outcomes were expanded to include associations with patient characteristics or subjective ratings of the interaction by observers. RESULTS We found 14 studies of verbal communication and 8 studies of nonverbal communication that met inclusion criteria. Verbal behaviors positively associated with health outcomes included empathy, reassurance and support, various patient-centered questioning techniques, encounter length, history taking, explanations, both dominant and passive physician styles, positive reinforcement, humor, psychosocial talk, time in health education and information sharing, friendliness, courtesy, orienting the patient during examination, and summarization and clarification. Nonverbal behaviors positively associated with outcomes included head nodding, forward lean, direct body orientation, uncrossed legs and arms, arm symmetry, and less mutual gaze. CONCLUSION Existing research is limited because of lack of consensus of what to measure, conflicting findings, and relative lack of empirical studies (especially of nonverbal behavior). Nonetheless, medical educators should focus on teaching and reinforcing behaviors known to be facilitative, and to continue to understand further how physician behavior can enhance favorable patient outcomes, such as understanding and adherence to medical regimens and overall satisfaction.