Miracle-dz/UniFAR-FTUs huggingface dataset:
A quantitative description of the peptide sharing between poliovirus and Homo sapiens

In the present study, we analyze the peptide commonality between poliovirus polyprotein and the human proteins. We report on the following findings: (1) the extent of polio peptide overlap on the human proteome is high, and involves the entire viral polyprotein; (2) viral peptide matching affects human proteins linked to fundamental cellular functions. The data may help to further our understanding of the relationships between poliovirus and the human host.
Laryngeal chondrosarcoma mimicking medullary thyroid carcinoma on fine‐needle aspiration cytology: A case report of a diagnostic pitfall

Chondrosarcoma (CS) of larynx is a rare laryngeal tumor accounting about 1% of laryngeal malignancies. When CS arises from thyroid cartilage, it may clinically present as a thyroid nodule. Here we report a rare case of CS of thyroid cartilage misinterpreted as medullary thyroid carcinoma. The main aim of this case report is to emphasize the important role of accurate clinical history, appropriate physical examination, and proper localization of the tumor and clear definitive imaging in conjunction with interpretation of cytologic smears. When any of these roles are unclear, it may result in misinterpretation of the cytologic smears. In these unusual circumstances, when cytomorphologic features does not completely fit an entity, communication with the physician and the consideration of a broad differential diagnoses in the head and neck pathology may lead to correct diagnosis and avoid diagnostic pitfalls. Also in certain conditions, ancillary studies including laboratory tests are necessary for definitive classification.
Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN

We present an efficient new method termed LN for propagating biomolecular dynamics according to the Langevin equation that arose fortuitously upon analysis of the range of harmonic validity of our normal-mode scheme LIN. LN combines force linearization with force splitting techniques and disposes of LIN’s computationally intensive minimization (anharmonic correction) component. Unlike the competitive multiple-timestepping (MTS) schemes today—formulated to be symplectic and time-reversible—LN merges the slow and fast forces via extrapolation rather than “impulses;” the Langevin heat bath prevents systematic energy drifts. This combination succeeds in achieving more significant speedups than these MTS methods which are limited by resonance artifacts to an outer timestep less than some integer multiple of half the period of the fastest motion (around 4–5 fs for biomolecules). We show that LN achieves very good agreement with small-timestep solutions of the Langevin equation in terms of thermodynamics (energy means and variances), geometry, and dynamics (spectral densities) for two proteins in vacuum and a large water system. Significantly, the frequency of updating the slow forces extends to 48 fs or more, resulting in speedup factors exceeding 10. The implementation of LN in any program that employs force-splitting computations is straightforward, with only partial second-derivative information required, as well as sparse Hessian/vector multiplication routines. The linearization part of LN could even be replaced by direct evaluation of the fast components. The application of LN to biomolecular dynamics is well suited for configurational sampling, thermodynamic, and structural questions.
Cardiac Memory: Diagnostic Tool in the Making

Classic definition of the term cardiac memory (CM) refers to the persistent T-wave changes on the ECG after a period of wide QRS rhythms that become evident once normal ventricular activation pattern is restored. It is related to the term ventricular electric remodeling sometimes used in basic science literature. Although CM itself is considered as an adaptive reaction to the change in the ventricular activation sequence, its manifestations (usually T-wave inversions, TWIs) are often confused with pathological conditions manifesting with TWI, such as myocardial ischemia or infarction. Although originally CM was described after restoration of the normal ventricular activation (narrow QRS), recently it was described and studied in wide QRS rhythms significantly expanding the clinical relevance of this phenomenon. Although complex molecular mechanisms of CM have been previously reviewed extensively, practical clinical application of this phenomenon received much less attention. In this article, we will focus on the clinically relevant aspects of CM including its diagnostic use in narrow and wide QRS rhythms. We will also examine how the fundamental CM property of being initiated by the changes in the geometry of the ventricular contraction might open new perspectives in wide QRST morphology analysis by establishing parallels between electric and mechanical functions of the heart. In 1915, White1 was the first to observe the phenomenon of transient TWI after single ventricular premature beats. Later in the 1940s, TWIs after conversion to sinus rhythm were described after paroxysmal tachycardias.2 Since then abnormal T waves of various duration have been documented after intermittent ventricular pre-excitation,3–5 ventricular pacing,6,7 intermittent left bundle branch block (LBBB),8,9 ventricular tachycardia,10 and even QRS widening associated with sodium channel blocker toxicity.11 In 1982, Rosenbaum et al10 introduced the term heart memory and presented the …
Age-Related Changes in Aortic Valve Hemostatic Protein Regulation

Objective— Although valvular endothelial cells have unique responses compared with vascular endothelial cells, valvular regulation of hemostasis is not well-understood. Heart valves remodel throughout a person’s lifetime, resulting in changes in extracellular matrix composition and tissue mechanical properties that may affect valvular endothelial cell hemostatic function. This work assessed valvular endothelial cell regulation of hemostasis in situ and in vitro as a function of specimen age. Approach and Results— Porcine aortic valves were assigned to 1 of 3 age groups: Young (YNG) (6 weeks); Adult (ADT) (6 months); or Elderly (OLD) (2 years). Histological examination of valves showed that secreted thrombotic/antithrombotic proteins localize at the valve endothelium and tissue interior. Gene expression and immunostains for von Willebrand factor (VWF), tissue factor pathway inhibitor, and tissue plasminogen activator in YNG porcine aortic valve endothelial cells were higher than they were for OLD, whereas plasminogen activator inhibitor 1 levels in OLD were higher than those for YNG and ADT. Histamine-stimulated YNG porcine aortic valve endothelial cells released higher concentrations of VWF proteins than OLD, and the fractions of VWF-140 fragments was not different between age groups. A calcific aortic valve disease in vitro model using valvular interstitial cells confirmed that VWF in culture significantly increased valvular interstitial cell nodule formation and calcification. Conclusions— Hemostatic protein regulation in aortic valve tissues and in valvular endothelial cells changes with age. The presence of VWF and other potential hemostatic proteins increase valvular interstitial cell calcification in vitro. Therefore, the increased capacity of elderly valves to sequester the hemostatic proteins, together with age-associated loss of extracellular matrix organization, warrants investigation into potential role of these proteins in the formation of calcific nodules.
Co-cultivation of Sorangium cellulosum strains affects cellular growth and biosynthesis of secondary metabolite epothilones.

Sorangium cellulosum, a cellulolytic myxobacterium, is capable of producing a variety of bioactive secondary metabolites. Epothilones are anti-eukaryotic secondary metabolites produced by some S. cellulosum strains. In this study, we analyzed interactions between 12 strains of S. cellulosum consisting of epothilone-producers and non-epothilone producers isolated from two distinct soil habitats. Co-cultivation on filter papers showed that different Sorangium strains inhibited one another's growth, whereas epothilone production by the producing strains changed markedly for most (73%) pairwise mixtures. Using a quantitative polymerase chain reaction, we demonstrated that the expression of epothilone biosynthetic genes in the epothilone producers typically changed significantly when these bacteria were mixed with non-producing strains. The results indicated that intraspecies interactions between different S. cellulosum strains not only inhibited the growth of partners, but also could change epothilone production.
Pitch Range Variation in English Tonal Contrasts: Continuous or Categorical?

Abstract The importance of pitch range variation for intonational meaning and theory is well known; however, whether pitch range is a phonetic dimension which is treated categorically in English remains unclear. To test this possibility, three intonation continua varying in pitch range were constructed which had endpoints with contrastive representations under autosegmental-metrical (AM) theory: H* vs. L+H*, H* with ‘peak delay’ vs. L*+H, and %H L* vs. L*. The prediction derived from AM theory was that the reproduction of continuous pitch range variation should show a discrete pattern reflecting a change in the phonological representation of tonal sequences and in the number of tonal targets across each continuum. Participants’ reproductions of each stimulus set showed continuous variation in pitch range, suggesting that pitch range is a gradient phonetic dimension in English conveying semantic contrast, similar to the formant space for vowels. Moreover, the gradience observed in productions across all parts of the pitch range suggests that contours within each series had the same number of tonal targets. The results support a version of AM theory in which rises and falls are usually comprised of two tonal targets, with strictly monotonic f₀ interpolation between them.
Protein-Losing Enteropathy in Systemic Lupus Erythematosus: 12 Years Experience from a Chinese Academic Center

Objective Protein-losing enteropathy (PLE) is a complication in some systemic lupus erythematosus (SLE) patients that is often misdiagnosed. With this study, we provide insight into clinical characteristics, laboratory characteristics, diagnostic tests, risk factors, treatment, and prognosis of the disease. Methods A retrospective, case-control study was performed in 44 patients with SLE-related PLE (PLE group) and 88 patients with active SLE (control group) admitted to our care from January 2000−January 2012. Risk factors for SLE-related PLE were examined, and we analyzed the accuracy of single and combined laboratory characteristics in discriminating SLE-related PLE from active SLE. Serum albumin and C3 levels were measured as outcome during and after treatment with corticosteroids and immunosuppressive agents. Results The PLE group had lower mean serum albumin and 24-hour urine protein levels, higher mean total plasma cholesterol levels, and greater frequencies of anti-SSA and SSB seropositivity compared with the control group. Anti-SSA seropositivity, hypoalbuminemia, and hypercholesterolemia were independent risk factors for SLE-related PLE. The simultaneous presence of serum albumin (<22 g/l) and 24-hour urine protein (<0.8 g/24 h) had high specificity, positive predictive value, negative predictive value, and positive likelihood ratio, a low negative likelihood ratio and no significant reduction in sensitivity. High dosage of glucocorticosteroid combined with cyclophosphomide were mostly prescribed for SLE-related PLE. Conclusion SLE-related PLE should be considered when an SLE patient presents with generalized edema, anti-SSA antibody seropositivity, hypercholesterolemia, severe hypoalbuminemia, and low 24-hour urine protein levels. Aggressive treatment for lupus might improve prognosis.
Cysteine String Protein Is Required for Calcium Secretion Coupling of Evoked Neurotransmission in Drosophila But Not for Vesicle Recycling

The entire deletion of the cysteine string protein (CSP) gene causes a temperature-sensitive (ts) block of evoked neurotransmission in Drosophila. CSP has been found to interact in vitro with the clathrin-uncoating ATPase HSC70, suggesting a potential role of CSP in vesicle recycling. Using FM1-43 imaging, we analyzed whether the ts block of neurotransmission incsp mutants is caused by a defect in vesicle exocytosis or vesicle recycling. We determined that FM1-43-labeled synaptic boutons of csp mutant neuromuscular junctions fail to destain at 32°C after K+ depolarization, and that FM1-43 dye uptake cannot be evoked by K+ stimulation at 32°C. However, when we stimulated dye uptake independent of depolarization by using black widow spider venom (BWSV), we observed endocytotic uptake of FM1-43. This suggests that endocytosis exhibits no primary ts defect. In addition, we found no ts defect of vesicle recycling at 32°C that would correlate with the ts block of neurotransmission. We also discovered that BWSV and the calcium ionophore calcimycin stimulate FM1-43 destaining and quantal release incsp mutants at 32°C when depolarization fails to evoke any response. The wild-type-like, calcimycin-induced response incsp null mutants indicates that some aspect of the depolarization-dependent calcium signaling pathway must be impaired, either calcium entry, calcium action, or both. Collectively, our results indicate that the csp mutation affects calcium secretion coupling of evoked exocytosis but not vesicle recycling. This supports the hypothesis that CSP links synaptic vesicles to calcium secretion coupling.
A note on the nearest neighbor in growth-restricted metrics

In this paper, we give results relevant to sequential and distributed dynamic data structures for finding nearest neighbors in growth-restricted metrics. Our sequential data structure uses linear space, and requires O(log n) queries in expecation and O(log n) queries for lookups with high probability. This improves the results of Karger and Ruhl [4], whose data structure uses O(n log n) space with comparable expected time bounds. This also improves on the time bound of a load-balanced version of algorithm (for dynamic networks) presented in [3]. Our algorithm was inspired by the object location data structure developed by Plaxton, Rajaraman and Richa [6], and is similar in structure to the algorithm of Krauthgamer and Lee [5]. It is significantly different that of Karger and Ruhl [4]. A distributed version of the algorithm presented here is in use as a part of Tapestry [3, 8], a peer-to-peer object location system based on [6].
From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and editing, and regulatory module activity. Despite great progress recently, substantial challenges remain, including discriminating biological variation from technical noise. Here we apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878. By using spike-in quantification standards, we estimate the absolute number of RNA molecules per cell for each gene and find significant variation in total mRNA content: between 50,000 and 300,000 transcripts per cell. We directly measure technical stochasticity by a pool/split design and find that there are significant differences in expression between individual cells, over and above technical variation. Specific gene coexpression modules were preferentially expressed in subsets of individual cells, including one enriched for mRNA processing and splicing factors. We assess cell-to-cell variation in alternative splicing and allelic bias and report evidence of significant differences in splice site usage that exceed splice variation in the pool/split comparison. Finally, we show that transcriptomes from small pools of 30–100 cells approach the information content and reproducibility of contemporary RNA-seq from large amounts of input material. Together, our results define an experimental and computational path forward for analyzing gene expression in rare cell types and cell states.
A randomized, double-blind comparison of lumbar epidural and intravenous fentanyl infusions for postthoracotomy pain relief. Analgesic, pharmacokinetic, and respiratory effects.

Although epidural opioids frequently are used to provide postoperative analgesia, several articles have suggested that the analgesia after epidural fentanyl is similar to that after an equal dose of fentanyl given intravenously. To address this issue further, 29 postthoracotomy patients were studied in a randomized, double-blinded trial comparing a lumbar epidural fentanyl infusion with an intravenous fentanyl infusion for analgesia, plasma fentanyl pharmacokinetics, and respiratory effects for 20 h postoperatively. In all patients in both groups, good analgesia was achieved (pain score less than 3, maximum 10) over a similar time course, although the patients receiving epidural infusion required a significantly larger fentanyl infusion dose than did the patients receiving intravenous infusion (group receiving epidural fentanyl infusion: 1.95 +/- 0.45 micrograms.kg-1.h-1; group receiving intravenous fentanyl infusion: 1.56 +/- 0.36 micrograms.kg-1.h-1; P = 0.0002). The time course for the plasma fentanyl concentrations was similar in the two groups, and plasma fentanyl concentrations were not significantly different at any sampling period (T7-T20; group receiving epidural fentanyl infusion: 1.8 +/- 0.5 ng/ml; group receiving intravenous fentanyl infusion: 1.6 +/- 0.6 ng/ml; P = 0.06). Similarly, calculated clearance values for the two groups were not significantly different (group receiving epidural fentanyl infusion: 0.95 +/- 0.26 l.kg-1.h-1; group receiving intravenous fentanyl infusion: 0.87 +/- 0.25 l.kg-1.h-1; P = 0.3). Both groups demonstrated a similar degree of mild to moderate respiratory depression postoperatively, which was assessed with continuous respiratory inductance plethysmography and sequential arterial blood gas analysis. Side effects (nausea, vomiting, pruritus) were mild and did not differ between groups. (ABSTRACT TRUNCATED AT 250 WORDS)
Accurate cross‒architecture performance modeling for sparse matrix‒vector multiplication (SpMV) on GPUs

This paper presents an integrated analytical and profile‒based cross‒architecture performance modeling tool to specifically provide inter‒architecture performance prediction for Sparse Matrix‒Vector Multiplication (SpMV) on NVIDIA GPU architectures. To design and construct the tool, we investigate the inter‒architecture relative performance for multiple SpMV kernels. For a sparse matrix, based on its SpMV kernel performance measured on a reference architecture, our cross‒architecture performance modeling tool can accurately predict its SpMV kernel performance on a target architecture. The prediction results can effectively assist researchers in making choice of an appropriate architecture that best fits their needs from a wide range of available computing architectures. We evaluate our tool with 14 widely‒used sparse matrices on four GPU architectures: NVIDIA Tesla C2050, Tesla M2090, Tesla K20m, and GeForce GTX 295. In our experiments, Tesla C2050 works as the reference architecture, the other three are used as the target architectures. For Tesla M2090, the average performance differences between the predicted and measured SpMV kernel execution times for CSR, ELL, COO, and HYB SpMV kernels are 3.1%, 5.1%, 1.6%, and 5.6%, respectively. For Tesla K20m, they are 6.9%, 5.9%, 4.0%, and 6.6% on the average, respectively. For GeForce GTX 295, they are 5.9%, 5.8%, 3.8%, and 5.9% on the average, respectively. Copyright © 2014 John Wiley & Sons, Ltd.
Extraskeletal myxoid chondrosarcoma. A clinicopathological study

Extraskeletal myxoid chondrosarcoma is a rare tumor of cartilagenous origin, with only 41 previously reported cases. It has a distinctive histologic pattern and should be distinguished from chondrosarcoma of bone because of its different behavioral pattern. The light microscopic, histo‐chemical and electron microscopic features of such a tumor are reported.
Capacity Management and Demand Prediction for Next Generation Data Centers

Advances in server, network, and storage virtualization are enabling the creation of resource pools of servers that permit multiple application workloads to share each server in the pool. This paper proposes and evaluates aspects of a capacity management process for automating the efficient use of such pools when hosting large numbers of services. We use a trace based approach to capacity management that relies on i) a definition for required capacity, ii) the characterization of workload demand patterns, iii) the generation of synthetic workloads that predict future demands based on the patterns, and iv) a workload placement recommendation service. A case study with 6 months of data representing the resource usage of 139 workloads in an enterprise data center demonstrates the effectiveness of the proposed capacity management process. Our results show that when consolidating to 8 processor systems, we predicted future per-server required capacity to within one processor 95% of the time. The approach enabled a 35% reduction in processor usage as compared to today's current best practice for workload placement.
Pharmacognostic and phytochemical studies on the rhizome of Nardostachys jatamansi DC. using different extracts.

Introduction: Nardostachys jatamansi DC. is an important ayurvedic plant. The root and rhizome contain active compounds with carminative, sedative, antispasmodic and tranquilizing properties. It is also used as an insect repellent. Essential oil from the drug shows antimicrobial activity against a number of microorganisms. Method: The present study comprises microscopic and macroscopic studies, phyto-chemical, physic-chemical, fluorescence, HPTLC analysis and microbial load estimation of the rhizome. Conclusion: Different extracts showed difference in presence of phyto-chemical constituents and physicochemical properties but chromatographic studies showed that all extracts contained valtrate. The study will provide referential information for the correct identification of the crude drug and establish pharmacopeial standards.
A Study of the Saturation of Analogical Grids Agnostically Extracted from Texts

Analogical grids aim to capture the organization of the lexicon of a language. We conduct experiments on analogical grids extracted in four diﬀerent languages with diﬀerent morphological richness. We study the saturation of analogical grids against their size. We observe that the logarithm of the saturation of an analogical grid is linear in the logarithm of its size. More surprisingly, the coeﬃcients of this log-log linear relation are extremely close across all four languages, even when the size or the genre of the corpus vary
Aging and ESRD Demographics: Consequences for the Practice of Dialysis

The disproportionate increase in the prevalence of chronic kidney disease (CKD) and end‐stage renal disease (ESRD) in the elderly is now recognized as a national and global reality. Among the major contributing factors are the aging of the population, a growing prevalence of CKD, greater access to care, and increased comorbidities. The utilization of renal replacement therapy in the geriatric population has concomitantly increased. It is imposing enormous challenges to the practice of ESRD care, the largest of which may be to determine the best application of clinical performance targets to a population with limitations in life expectancy. Concurrently, increased focus on quality of life will be required. The effective dialysis practitioner will need to adapt to the aging ESRD demographics with an increased focus on physical and mental well‐being of the geriatric patient.