Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome

The genus Sinorhizobium/Ensifer mostly groups nitrogen-fixing bacteria that create root or stem nodules on leguminous plants and transform atmospheric nitrogen into ammonia, which improves the productivity of the plants. Although these biotechnologically-important bacteria are commonly found in various soil environments, little is known about their phages. In this study, the genome of Sinorhizobium sp. LM21 isolated from a heavy-metal-contaminated copper mine in Poland was investigated for the presence of prophages and DNA methyltransferase-encoding genes. In addition to the previously identified temperate phage, ΦLM21, and the phage-plasmid, pLM21S1, the analysis revealed the presence of three prophage regions. Moreover, four novel phage-encoded DNA methyltransferase (MTase) genes were identified and the enzymes were characterized. It was shown that two of the identified viral MTases methylated the same target sequence (GANTC) as cell cycle-regulated methyltransferase (CcrM) of the bacterial host strain, LM21. This discovery was recognized as an example of the evolutionary convergence between enzymes of sinorhizobial viruses and their host, which may play an important role in virus cycle. In the last part of the study, thorough comparative analyses of 31 sinorhizobial (pro)phages (including active sinorhizobial phages and novel putative prophages retrieved and manually re-annotated from Sinorhizobium spp. genomes) were performed. The networking analysis revealed the presence of highly conserved proteins (e.g., holins and endolysins) and a high diversity of viral integrases. The analysis also revealed a large number of viral DNA MTases, whose genes were frequently located within the predicted replication modules of analyzed prophages, which may suggest their important regulatory role. Summarizing, complex analysis of the phage protein similarity network enabled a new insight into overall sinorhizobial virome diversity.
Early Clinical Assessment of the Antimicrobial Activity of Finafloxacin Compared to Ciprofloxacin in Subsets of Microbiologically Characterized Isolates

ABSTRACT Two phase II studies were performed with patients with uncomplicated urinary tract infections (uUTIs) and complicated urinary tract infections (cUTIs) or acute pyelonephritis (PN) to compare finafloxacin (300 mg twice a day [b.i.d.] orally for uUTI and 800 mg once a day [q.d.] intravenously [i.v.] for cUTI/PN) and ciprofloxacin (250 mg b.i.d. orally for uUTI and 400 mg b.i.d. i.v. for cUTI/PN). The early response to the study medications was evaluated in the microbiological intent-to-treat population (mITT) at day 3. A total of 21% of the isolates were ciprofloxacin resistant, 13.7% were primed pathogens carrying a mutation(s) potentially fostering fluoroquinolone resistance development, and 7.1% produced extended-spectrum β-lactamases (ESBLs). Finafloxacin demonstrated very good early clinical activity, with microbiological eradication rates of 88.6% (n = 132), compared to 78.7% (n = 61) for ciprofloxacin, and 69.6% (n = 23), compared to 35.7% (n = 14) for ciprofloxacin, in patients with ciprofloxacin-resistant uropathogens; 94.1% (n = 17), compared to 80.0% (n = 10) for ciprofloxacin, in patients infected with uropathogens primed for fluoroquinolone resistance uropathogens; and 91.7% (n = 11), compared to 0% for ciprofloxacin, in patients infected with ESBL producers. Finafloxacin demonstrated early and rapid activity against uropathogens, including fluoroquinolone-resistant and/or multiresistant pathogens or ESBL producers, while ciprofloxacin was less active against this subset of resistant pathogens. Susceptibilities of pathogens were quantitated by broth microdilution. Isolates were subgrouped according to their susceptibility patterns, in particular first-step quinolone resistance, quinolone resistance, and ESBL production. Eradication was defined as the elimination or reduction of study entry pathogens to <103 CFU/ml in urine culture. (The studies described in this paper have been registered at ClinicalTrials.gov under identifiers NCT00722735 and NCT01928433.)
Mechanism Underlying Acupuncture-Ameliorated Depressive Behaviors by Enhancing Glial Glutamate Transporter in Chronic Unpredictable Mild Stress (CUMS) Rats

Background Major depressive disorder (MDD) is a recurrent mental illness worldwide. The glutamatergic neurotransmission system is now a target for antidepressant therapy because it takes part in synaptic plasticity and cognition in physical condition and has a potential excitatory neurotoxicity in pathological conditions. Glial glutamate transporter EAAT2 performs 90% of Glu neurotransmission. Therefore, the aim of the study was to evaluate the effect of acupuncture on depressive behaviors and EAAT2 in CUMS. Material/Methods We randomly divided 56 male SD rats into a normal group, a model group, an acupuncture group, and a riluzole group. Rats in the model group, acupuncture group, and riluzole group underwent chronic unpredictable mild stress (CUMS) exposure for 21 days. The acupuncture group received electro-acupuncture stimulation on LI4 and LR3 for 5 continuous days per week for 4 weeks, and rats in the riluzole group received 4 mg/kg of riluzole orally (Sanofi, J20140092) for 4 weeks after undergoing CUMS stimulation. Results Rats showed significantly increased sucrose consumption in the sucrose preference test paradigm, and showed elevated food intake and shortened latency in the novelty-suppressed feeding test paradigm after undergoing acupuncture therapy and riluzole treatment. The amelioration of depressive behavioral actions was consistent with increasing number of positive cells, protein, and mRNA expression of glial glutamate transporter EAAT2 in the hippocampus and PFC. Conclusions The results suggest that acupuncture and riluzole are both effective in improving sucrose consumption, latency, and food intake in CUMS rats. However, acupuncture appears to achieve an antidepressant effect later than riluzole does because it might need accumulated stimulation by enhancing EAAT2 expression. Enhance glial glutamate transporter EAAT2 in the hippocampus and PFC is a mechanism underlying the antidepressant effect of acupuncture.
Effect of metabolic acidosis on NaCl transport in the proximal tubule

Wang, Tong, Allan L. Egbert, Jr., Peter S. Aronson, and Gerhard Giebisch. Effect of metabolic acidosis on NaCl transport in the proximal tubule. Am. J. Physiol. 274 (Renal Physiol. 43): F1015–F1019, 1998. —In metabolic acidosis, the capacity of the proximal tubule for bicarbonate absorption is enhanced, whereas NaCl reabsorption is inhibited. Recent evidence indicates that transcellular NaCl absorption in the proximal tubule is mediated by apical membrane Cl2/formate exchange and Cl2/oxalate exchange, in parallel with recycling of these organic anions. We evaluated whether the effect of metabolic acidosis to inhibit NaCl reabsorption in the proximal tubule is due at least in part to inhibition of organic anion-dependent NaCl transport in this nephron segment. Absorption rates of bicarbonate (JHCO3), chloride (JCl), and fluid (Jv) were measured in rat proximal tubule segments microperfused in situ. We confirmed that metabolic acidosis stimulates JHCO3 in tubules microperfused with 25 mM HCO3 , pH 7.4. For measurements of JCl, tubules were microperfused with a low-bicarbonate (5 mM), high-chloride solution, simulating conditions in the late proximal tubule. Under these conditions, baseline JCl and Jv measured in the absence of formate and oxalate were not significantly different between control and acidotic rats. However, whereas addition of 50 μM formate or 1 μM oxalate to luminal and capillary perfusates markedly stimulated JCl and Jv in control rats, formate and oxalate failed to stimulate JCl and Jv in acidotic rats. We conclude that metabolic acidosis markedly downregulates organic anion-stimulated NaCl absorption, thereby allowing differential regulation of proximal tubule NaHCO3 and NaCl transport.
Stable isotopes of Hawaiian spiders reflect substrate properties along a chronosequence

The Hawaiian Islands offer a unique opportunity to test how changes in the properties of an isolated ecosystem are propagated through the organisms that occur within that ecosystem. The age-structured arrangement of volcanic-derived substrates follows a regular progression over space and, by inference, time. We test how well documented successional changes in soil chemistry and associated vegetation are reflected in organisms at higher trophic levels—specifically, predatory arthropods (spiders)—across a range of functional groups. We focus on three separate spider lineages: one that builds capture webs, one that hunts actively, and one that specializes on eating other spiders. We analyze spiders from three sites across the Hawaiian chronosequence with substrate ages ranging from 200 to 20,000 years. To measure the extent to which chemical signatures of terrestrial substrates are propagated through higher trophic levels, we use standard stable isotope analyses of nitrogen and carbon, with plant leaves included as a baseline. The target taxa show the expected shift in isotope ratios of δ15N with trophic level, from plants to cursorial spiders to web-builders to spider eaters. Remarkably, organisms at all trophic levels also precisely reflect the successional changes in the soil stoichiometry of the island chronosequence, demonstrating how the biogeochemistry of the entire food web is determined by ecosystem succession of the substrates on which the organisms have evolved.
Date field extraction from handwritten documents using HMMs

Automatic document interpretation and retrieval is an important task to access handwritten digitized document repositories. In documents, the date is an important field and it has various applications such as date-wise document indexing/retrieval. In this paper a framework has been proposed for automatic date field extraction from handwritten documents. In order to design the system, sliding window-wise Local Gradient Histogram (LGH)-based features and a character-level Hidden Markov Model (HMM)-based approach have been applied for segmentation and recognition. Individual date components such as month-word (month written in word form i.e. January, Jan, etc.), numeral, punctuation and contraction categories are segmented and labelled from a text line. Next, a Histogram of Gradient (HoG)-based features and a Support Vector Machine (SVM)- based classifier have been used to improve the results obtained from the HMM-based recognition system. Subsequently, both numeric and semi-numeric regular expressions of date patterns have been considered for undertaking date pattern extraction in labelled components. The experiments are performed on an English document dataset and the encouraging results obtained from the approach indicate the effectiveness of the proposed system.
Strength and Conditioning Coaches’ Application of the Session Rating of Perceived Exertion Method of Monitoring within Professional Rugby Union

Abstract Session rating of perceived exertion (session-RPE) is a method of monitoring and managing training loads. The purpose of this study was to research how and for what purpose strength and conditioning (S&C) coaches implement this monitoring method within professional rugby union. The study also aimed to assess if S&C coaches found this monitoring method to be valid and effective. An online survey containing 24 fixed response questions was used to assess how S&C coaches applied the session-RPE method. The survey was piloted with expert researchers and practitioners in the area of session-RPE prior to distribution and alterations were made to the survey based on the experts’ feedback. Twenty S&C coaches working with professional rugby union clubs in Ireland, England, Scotland and Wales completed the survey. The coaches’ responses indicated that the majority found the session-RPE to be a valid and effective monitoring method. While some good implementation practices were identified, not all of the coaches adhered to these guidelines which may impact on the accuracy of the collected data. For example, 30% of coaches do not collect the RPE for every session that a player does per week limiting the use of the session-RPE variables cumulative training load, training monotony, training strain and acute:chronic load ratio. S&C coaches within rugby should consider using session-RPE as a method of monitoring and implement the method in a manner reflective of research findings to enhance the potential applications of this system in maximising adaptations and minimising the risk of injury.
Fluorene‐containing tetraphenylethylene molecules as lasing materials

ABSTRACT A series of star‐shaped oligofluorene molecules, each containing a TPE core, have been specifically designed and produced to show effective aggregation‐induced emission (AIE). Each molecule differs either in the number of fluorene units within the arms (e.g., 1 or 4, compounds 4 and 5), or the terminal group positioned at the end of each arm (e.g., H, TMS, or TPA, compounds 4, 6, and 7). Although they are all poor emitters in solution phase they become efficient yellow‐green luminogens in the condensed state. Their AIE properties were investigated in THF/H2O mixtures, with each molecule exhibiting a clear emission enhancement at specific water contents. An all‐organic distributed feedback (DFB) laser was fabricated using compound 4 as the gain material and exhibited an average threshold energy fluence of 60 ± 6 μJ/cm2 and emission in the green region. Furthermore, piezofluorochromism studies on a thin film of this material displayed a linear dependence of the amplified spontaneous emission (ASE) peak position on applied pressure, indicating potential applications as lasing‐based pressure sensors. © 2016 The Authors. Journal of Polymer Science Part A: Polymer Chemistry Published by Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 734–746
MRTuner: A Toolkit to Enable Holistic Optimization for MapReduce Jobs

MapReduce based data-intensive computing solutions are increasingly deployed as production systems. Unlike Internet companies who invent and adopt the technology from the very beginning, traditional enterprises demand easy-to-use software due to the limited capabilities of administrators. Automatic job optimization software for MapReduce is a promising technique to satisfy such requirements. In this paper, we introduce a toolkit from IBM, called MRTuner, to enable holistic optimization for MapReduce jobs. In particular, we propose a novel Producer-Transporter-Consumer (PTC) model, which characterizes the tradeoffs in the parallel execution among tasks. We also carefully investigate the complicated relations among about twenty parameters, which have significant impact on the job performance. We design an efficient search algorithm to find the optimal execution plan. Finally, we conduct a thorough experimental evaluation on two different types of clusters using the HiBench suite which covers various Hadoop workloads from GB to TB size levels. The results show that the search latency of MRTuner is a few orders of magnitude faster than that of the state-of-the-art cost-based optimizer, and the effectiveness of the optimized execution plan is also significantly improved.
An IUE Atlas of Pre-Main-Sequence Stars. II. Far-Ultraviolet Accretion Diagnostics in T Tauri Stars

We use our ultraviolet (UV) atlas of pre-main-sequence stars constructed from all useful, short-wavelength, low-resolution spectra in the International Ultraviolet Explorer (IUE) satellite Final Archive to analyze the short-wavelength UV properties of 49 T Tauri stars (TTSs). We compare the line and continuum fluxes in these TTSs with each other and with previously published parameters of these systems, including rotation rate, infrared excess, and mass accretion rate. The short-wavelength continuum in the classical TTSs (CTTSs) appears to originate in a ~10,000 K optically thick plasma, while in the naked TTSs (NTTSs—stars without dusty disks) the continuum appears to originate in the stellar atmosphere. We show that all of the TTSs in our sample lie in the regime of "saturated" magnetic activity due to their small Rossby numbers. However, while some of the TTSs show emission line surface fluxes consistent with this saturation level, many CTTSs show significantly stronger emission than predicted by saturation. In these stars, the emission line luminosity in the high ionization lines present in the spectrum between 1200 and 2000 Å correlates well with the mass accretion rate. Therefore, we conclude that the bulk of the short-wavelength emission seen in CTTSs results from accretion related processes and not from dynamo-driven magnetic activity. Using CTTSs with known mass accretion rates, we calibrate the relationship between and L to derive the mass accretion rate for some CTTSs which for various reasons have never had their mass accretion rates measured. Finally, several of the CTTSs show strong emission from molecular hydrogen. While emission from H2 cannot form in gas at a temperature of ~105 K, the strength of the molecular hydrogen emission is nevertheless well correlated with all the other emissions displayed in the IUE short-wavelength bandpass. This suggests that the H2 emission is in fact fluorescent emission pumped by the emission (likely Lyα) from hotter gas.
COUPLED LONGITUDINAL 1-D THERMAL AND VISCOELASTIC WAVES IN MEDIA WITH TEMPERATURE DEPENDENT MATERIAL PROPERTIES

A general analysis is formulated for the closed loop coupled thermal and displacement viscoelastic 1–D wave problem. The proper inclusion of the highly temperature sensitive viscoelastic material properties renders the problem nonlinear, even though the displacements and material properties continue to obey linear relations. Various categories of open and closed loop temperature-displacement couplings as well as boundary conditions are formulated and discussed. Comparisons between temperature independent and dependent material properties indicate that the nature of the latter nonlinear problem radically differs from the former steady-state temperature linear one.
Characteristics and demographics of reversible cerebral vasoconstriction syndrome: A large prospective series of Korean patients

Objectives To report demographics and characteristics of reversible cerebral vasoconstriction syndrome (RCVS) in the Korean cohort. Methods We prospectively recruited patients with definite (imaging-proven) RCVS and probable (imaging-negative) RCVS who visited Samsung Medical Center between June 2012 and September 2016. Clinical manifestations, neuroimaging, treatment, and clinical outcomes were evaluated in all patients. Characteristics of RCVS without typical causes (“idiopathic RCVS”) were compared with those of RCVS with identifiable causes (“secondary RCVS”). International Classification of Headache Disorders (ICHD)-3 beta criteria for 6.7. 3 RCVS and 6.7. 3.1 probable RCVS were tested. Results A total of 138 patients (104 definite and 34 probable RCVS) were included in this study. Patients with definite RCVS were predominantly female (85.6%) and middle-aged (mean, 50.7 [range, 23–82] years). Probable RCVS was associated with less female predominance (70.6%, p = 0.049), more typical manifestations (p < 0.001), and none of neurological complications. One-hundred and one (97.1%) patients with definite RCVS had headache, but the typical “recurrent and/or triggered” thunderclap headache was reported in only 83 (82.2%). In most patients with definite RCVS (84.6%), RCVS was idiopathic, while only 16 (15.4%) had secondary causes. Compared to those with secondary RCVS, patients with idiopathic RCVS were older (52.8 ± 11.42 vs. 39.1 ± 9.55 years, p < 0.001). Patients with secondary RCVS had more complications than those with idiopathic RCVS (40.5% vs. 12.5%, p = 0.018). Among idiopathic RCVS patients, 33 (37.5%) reported a preceding event or a change in lifestyle, environment, health, or medication within one month before onset. Conclusion In our cohort, RCVS was benign and idiopathic in most patients, and occurred frequently in middle-aged women. Manifestations of RCVS were more diverse than previously recognized, and forms without any headache existed. Different genetic, social, and environmental factors should be taken into account to unveil the spectrum and pathophysiology of RCVS.
An implantable wireless optogenetic stimulation system for peripheral nerve control

An implantable wireless optogenetic stimulation system with an LED-based optical stimulation cuff electrode was developed for peripheral nerve control. The proposed system consisted of a battery-powered optical cuff electrode, optical stimulation controller, and wireless communication system. The optical cuff electrode had a polydimethylsiloxane (PDMS) structure was designed to illuminate the entire sciatic nerve. The wireless communication system was designed to comply with medical implant communication service (MICS) regulations. To evaluate the proposed system, optogenetic stimulation was performed in optogenetic transgenic mice (Thy1::ChR2). The optical cuff electrode was implanted on the sciatic nerve, and movement was elicited during optical stimulation. The experimental results show that ankle movement can be generated wirelessly using optical stimulation pulse parameters.
GLP-1 slows solid gastric emptying and inhibits insulin, glucagon, and PYY release in humans.

The aim of the present study was to assess the effect of glucagon-like peptide-1 (GLP-1) on solid gastric emptying and the subsequent release of pancreatic and intestinal hormones. In eight men [age 33.6 ± 2.5 yr, body mass index 24.1 ± 0.9 (means ± SE)], scintigraphic solid gastric emptying during infusion of GLP-1 (0.75 pmol ⋅ kg-1 ⋅ min-1) or saline was studied for 180 min. Concomitantly, plasma concentrations of C- and N-terminal GLP-1, glucose, insulin, C-peptide, glucagon, and peptide YY (PYY) were assessed. Infusion of GLP-1 resulted in a profound inhibition of both the lag phase (GLP-1: 91.5, range 73.3-103.6 min vs. saline: 19.5, range 10.2-43.4 min) and emptying rate (GLP-1: 0.34, range 0.06-0.56 %/min vs. saline: 0.84, range 0.54-1.33 %/min; P< 0.01 for both) of solid gastric emptying. Concentrations of both intact and total GLP-1 were elevated to supraphysiological levels. Plasma glucose and glucagon concentrations were below baseline during infusion of GLP-1 in contrast to saline infusion, where concentrations were elevated above baseline (both P< 0.001). The insulin and C-peptide responses were lower during infusion with GLP-1 than with saline ( P < 0.004 and P < 0.001, respectively). Plasma PYY concentrations decreased below baseline during GLP-1 infusion in contrast to saline, where concentrations were elevated above baseline ( P = 0.04). Infusion of GLP-1 inhibits solid gastric emptying with secondary effects on the release of insulin, C-peptide, and glucagon, resulting in lower plasma glucose concentrations. In addition, the release of PYY into the circulation is inhibited by GLP-1 infusion, suggesting a negative feedback of GLP-1 on the function of the L-cell.