Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Clostridium difficile: Clonality and Pathogenicity Locus Diversity

Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings. The major virulence determinants are large clostridial toxins, toxin A (tcdA) and toxin B (tcdB), encoded within the pathogenicity locus (PaLoc). Isolates vary in pathogenicity from hypervirulent PCR-ribotypes 027 and 078 with high mortality, to benign non-toxigenic strains carried asymptomatically. The relative pathogenicity of most toxigenic genotypes is still unclear, but may be influenced by PaLoc genetic variant. This is the largest study of C. difficile molecular epidemiology performed to date, in which a representative collection of recent isolates (n = 1290) from patients with CDI in Oxfordshire, UK, was genotyped by multilocus sequence typing. The population structure was described using NeighborNet and ClonalFrame. Sequence variation within toxin B (tcdB) and its negative regulator (tcdC), was mapped onto the population structure. The 69 Sequence Types (ST) showed evidence for homologous recombination with an effect on genetic diversification four times lower than mutation. Five previously recognised genetic groups or clades persisted, designated 1 to 5, each having a strikingly congruent association with tcdB and tcdC variants. Hypervirulent ST-11 (078) was the only member of clade 5, which was divergent from the other four clades within the MLST loci. However, it was closely related to the other clades within the tcdB and tcdC loci. ST-11 (078) may represent a divergent formerly non-toxigenic strain that acquired the PaLoc (at least) by genetic recombination. This study focused on human clinical isolates collected from a single geographic location, to achieve a uniquely high density of sampling. It sets a baseline of MLST data for future comparative studies investigating genotype virulence potential (using clinical severity data for these isolates), possible reservoirs of human CDI, and the evolutionary origins of hypervirulent strains.
Cadaver Dissection Is Obsolete in Medical Training! A Misinterpreted Notion

Cadaver dissection (CD) is considered a tool for studying the structural details of the human body. Lately, conflicting opinions regarding the utility of this modality in medical training have been published in medical literature. This review of the literature examines the status of anatomy teaching with CD in traditional, modern, and postgraduate medical training across the world. Literature published in the English language on topics related to CD in the past 3 decades was scrutinized using different search engines. About 200 full texts were reviewed. We describe how medical schools have continued to include CD in anatomy teaching in the traditional or modified form. Medical schools that stopped or decreased CD have learnt from their experiences, and have restarted it in modified forms by integrating it vertically with medical training. In addition, CD activities have increased in postgraduate anatomy courses, surgery training, and voluntary/optional CD programs. CD, when integrated vertically, still has a part to play in medical training in modified ways. This overview may help curriculum designers to place CD in medical curricula and training programs in a justified manner.
Carotid‐cavernous fistula after endovascular intervention for chronic carotid artery total occlusion

In addition to head trauma and cranial surgery, endovascular intervention for chronic carotid artery occlusion (CAO) may also result in carotid‐cavernous fistula (CCF). The management and prognosis of iatrogenic CCF during CAO recanalization have never been well described and discussed in the literature.
The relationship between visual search and categorization of own‐ and other‐age faces

Young adult participants are faster to detect young adult faces in crowds of infant and child faces than vice versa. These findings have been interpreted as evidence for more efficient attentional capture by own-age than other-age faces, but could alternatively reflect faster rejection of other-age than own-age distractors, consistent with the previously reported other-age categorization advantage: faster categorization of other-age than own-age faces. Participants searched for own-age faces in other-age backgrounds or vice versa. Extending the finding to different other-age groups, young adult participants were faster to detect young adult faces in both early adolescent (Experiment 1) and older adult backgrounds (Experiment 2). To investigate whether the own-age detection advantage could be explained by faster categorization and rejection of other-age background faces, participants in experiments 3 and 4 also completed an age categorization task. Relatively faster categorization of other-age faces was related to relatively faster search through other-age backgrounds on target absent trials but not target present trials. These results confirm that other-age faces are more quickly categorized and searched through and that categorization and search processes are related; however, this correlational approach could not confirm or reject the contribution of background face processing to the own-age detection advantage.
Aerodynamic force and power for flapping wing at low reynolds number in ground effect

In the development of MAVs, small sized flapping wing designs mimicking insects have appeared recently and lot of studies have been carried out for various aspects of insect flight. The study of aerodynamics of ground effect is an important venue. In this paper CFD studies has been done to simulate the ground effect in hover flight for a rectangular wing. Various heights from very near to the ground till free stream condition where the ground effect is absent are investigated. Incompressible 3D NS equations are numerically solved and results are presented. Aerodynamic vertical force and aerodynamic power variation has been presented. The study indicates that during hover very near to the ground, average vertical force during a wing beat cycle increases largely as compared to its free stream condition in the absence of ground effect. For the typical case taken a 26% increase in average cycle vertical force and 11% decrease in average specific power is noted near the ground. Maximum vertical force increase is found below three quarters of wing length distance from the ground. The ground effect on aerodynamic force or power vanishes after 2.5 times the wing length height above the ground.
Hound

Stragglers are exceptionally slow tasks within a job that delay its completion. Stragglers, which are uncommon within a single job, are pervasive in datacenters with many jobs. A large body of research has focused on mitigating datacenter stragglers, but relatively little research has focused on systematically and rigorously identifying their root causes. We present Hound, a statistical machine learning framework that infers the causes of stragglers from traces of datacenter-scale jobs. Hound is designed to achieve several objectives: datacenter-scale diagnosis, interpretable models, unbiased inference, and computational efficiency. We demonstrate Hound's capabilities for a production trace from Google's warehouse-scale datacenters and two Spark traces from Amazon EC2 clusters.
Strength and deformation characteristics of engineered cementitious composite slabs with different polymer fibres

This paper presents a study on the compressive and flexural strength of engineered cementitious composite (ECC) cubes and slabs, reinforced with various polymer fibres. The type of fibre, fibre content and aspect ratio were the parameters considered in this study. For all types of fibre, the compressive strength of the ECC decreased as the reinforcing index increased. For the ECC polypropylene fibre (PP) slabs, the first crack strength significantly decreased with an increase in the fibre content. For the ECC polyethylene fibre (PE) slabs, the first crack strength decreased as the reinforcing index increased. For the ECC PE slabs, the usage of PE 1600D fibres showed a substantial increase in flexural strength due to their higher tensile strength and E modulus. The ECC PP slabs behaved like plane concrete due to the zero value of flexural strength, which was attributed to the weak interfacial bonding with the cement matrix, low tensile strength and E modulus of the PP fibres. The highest ductility was observed for the ECC-PE slabs with the highest recorded deflection values; these values achieved many extended multiple cracks and an extensive area under the load–deflection curve indicating high energy absorption capacity.
Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization

The process of protein misfolding and self-assembly into various, polymorphic aggregates is associated with a number of important neurodegenerative diseases. Only recently, crystal structures of several short peptides have provided detailed structural insights into -sheet rich aggregates, known as amyloid fibrils. Knowledge about early events of the formation and interconversion of small oligomeric states, an inevitable step in the cascade of peptide self-assembly, however, remains still limited. We employ molecular dynamics simulations in explicit solvent to study the spontaneous aggregation process of steric zipper peptide segments from the tau protein and insulin in atomistic detail. Starting from separated chains with random conformations, we find a rapid formation of structurally heterogeneous, -sheet rich oligomers, emerging from multiple bimolecular association steps and diverse assembly pathways. Furthermore, our study provides evidence that aggregate intermediates as small as dimers can be kinetically trapped and thus affect the structural evolution of larger oligomers. Alternative aggregate structures are found for both peptide sequences in the different independent simulations, some of which feature characteristics of the known steric zipper conformation (e.g., -sheet bilayers with a dry interface). The final aggregates interconvert with topologically distinct oligomeric states exclusively via internal rearrangements. The peptide oligomerization was analyzed through the perspective of a minimal oligomer, i.e., the dimer. Thereby all observed multimeric aggregates can be consistently mapped onto a space of reduced dimensionality. This novel method of conformational mapping reveals heterogeneous association and reorganization dynamics that are governed by the characteristics of peptide sequence and oligomer size.
Evidence for Lignin Oxidation by the Giant Panda Fecal Microbiome

The digestion of lignin and lignin-related phenolic compounds from bamboo by giant pandas has puzzled scientists because of the lack of lignin-degrading genes in the genome of the bamboo-feeding animals. We constructed a 16S rRNA gene library from the microorganisms derived from the giant panda feces to identify the possibility for the presence of potential lignin-degrading bacteria. Phylogenetic analysis showed that the phylotypes of the intestinal bacteria were affiliated with the phyla Proteobacteria (53%) and Firmicutes (47%). Two phylotypes were affiliated with the known lignin-degrading bacterium Pseudomonas putida and the mangrove forest bacteria. To test the hypothesis that microbes in the giant panda gut help degrade lignin, a metagenomic library of the intestinal bacteria was constructed and screened for clones that contained genes encoding laccase, a lignin-degrading related enzyme. A multicopper oxidase gene, designated as lac51, was identified from a metagenomic clone. Sequence analysis and copper content determination indicated that Lac51 is a laccase rather than a metallo-oxidase and may work outside its original host cell because it has a TAT-type signal peptide and a transmembrane segment at its N-terminus. Lac51 oxidizes a variety of lignin-related phenolic compounds, including syringaldazine, 2,6-dimethoxyphenol, ferulic acid, veratryl alcohol, guaiacol, and sinapinic acid at conditions that simulate the physiologic environment in giant panda intestines. Furthermore, in the presence of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringic acid, or ferulic acid as mediators, the oxidative ability of Lac51 on lignin was promoted. The absorbance of lignin at 445 nm decreased to 36% for ABTS, 51% for syringic acid, and 51% for ferulic acid after incubation for 10 h. Our findings demonstrate that the intestinal bacteria of giant pandas may facilitate the oxidation of lignin moieties, thereby clarifying the digestion of bamboo lignin by the animal.
Staging hand-wrist and cervical vertebrae images: a comparison of reproducibility.

OBJECTIVES The aim of this study was to compare the reproducibility of skeletal maturation assessments by raters with similar orthodontic experience using hand-wrist (HW) and cervical vertebral maturation (CVM) methods. METHODS HW and lateral cephalometric radiographs from 15 subjects (8 males and 7 females; ages, 9-16 years) were selected randomly. HW skeletal maturation was evaluated by the method of Greulich and Pyle, and CVM staging was evaluated by the method of Baccetti et al. Six orthodontic residents evaluated all images at three time periods: T1, initial evaluation; T2, re-evaluation after 7 days and T3, final evaluation after 5 weeks. Intra- and interexaminer reproducibility was evaluated with the intraclass correlation coefficient; the limits of agreement (LoA) were determined by using the Bland-Altman method. RESULTS The intraexaminer reliability assessed by intraclass correlation coefficient was scored as good for both of methods (T1-T2-T3 HW = 0.89 and CVM = 0.80; T1-T2 HW = 0.87 and CVM = 0.77; T2-T3 HW0 = 0.90 and CVM = 0.81), as well as the interexaminer evaluation, with the exception of HW-T1, which scored excellent (0.92). The width of LoA from Bland-Altman plot of cervical vertebra method was narrower (CVM T1-T2: -2.3 and +1.8; CVM T2-T3: -2.0 and +2.0) than the HW method (HW T1-T2: -3.9 and +4.8; HW T2-T3: -4.0 and +3.5). CONCLUSIONS Both HW and CVM methods presented good reproducibility for intra- and interexaminer correlation assessments. The small LoA indicated that the CVM is a reproducible method.
Radiosurgery of Glomus Tumors of Temporal Bone: a Meta-analysis.

OBJECTIVE 1) Perform a meta-analysis of the available data on the outcomes of stereotactic radiosurgery (SRS) for the treatment of temporal bone glomus tumors (GT), and 2) evaluate the collective outcomes of SRS treatment with respect to tumor control. DATA SOURCES A thorough literature search of the published English-language literature from 2011 to 2016 was performed in PubMed, Ovid, and Cochrane databases using the keywords ("Gamma Knife" or "CyberKnife" or "linear accelerator" or "radiosurgery") and ("glomus jugulare" or "jugular paraganglioma" or "glomus tympanicum"). STUDY SELECTION Studies reporting outcomes of SRS for temporal bone GT were included. DATA EXTRACTION Of 45 articles found, 15 studies met our inclusion and exclusion criteria and were selected for qualitative and quantitative analyses totaling 511 patients. DATA SYNTHESIS Average margin dose, modality, isodose line, volume decrease, follow-up duration, and tumor control rate data were extracted and analyzed. CONCLUSION Gamma Knife was the most commonly implemented radiosurgery modality and was used in eight studies. The mean marginal dose varied between 13.2 and 20 Gy. The pooled tumor control rate was 95.4% (95% CI: 93.6-97.2%) over a median follow-up duration ranging between 27.4 and 148 months. Clinical data on outcomes of SRS for the treatment of GTs are sparse and primarily limited to single institutional analyses, with considerable variation in tumor volume and follow-up duration. This meta-analysis provides an in-depth analysis of the available data in the literature and reviews the reported outcomes. Future studies on SRS for GT should include data on tumor growth before radiation as well as follow-up periods sufficiently long to identify true tumor control.
A new treatment for frostbite sequelae; Botulinum toxin

ABSTRACT Frostbite sequelae are a relevant occupational injury outcome for soldiers in arctic environments. A Caucasian male soldier suffered frostbite to both hands during a military winter exercise. He developed sensory-motor disturbances and cold hypersensitivity. Angiography and thermography revealed impaired blood flow while Quantitative Sensory Testing indicated impaired somato-sensory nerve function. Two years after the initial event, he received an off label treatment with Botulinum toxin distributed around the neurovascular bundles of each finger. After treatment, cold sensitivity was reduced while blood flow and somato-sensory nerve function improved. The successful treatment enabled the soldier to successfully pursue his career in the army.
Rheological Properties of Polystyrene/Supercritical CO2 Solutions from an Extrusion Slit Die

Recent advances in the use of supercritical CO 2 (scCO 2 ) in polymer processing (i.e. injection molding and extrusion) have increased the need for rheological data of polymer/scCO 2 solutions at high pressures. In this study, a slit die with a sudden contraction was used to investigate the entrance pressure drop as well as the shear and extensional viscosities of a polystyrene (PS) melt and of a PS/scCO 2 solution. Dissolution of CO 2 into the PS melt was shown to reduce its entrance pressure drop as well as its shear and extensional viscosities. The entrance pressure drop of PS and PS/CO 2 was found to be a strong (exponential) function of pressure. The entrance pressure drop as a function of wall shear stress could be fitted with a master curve for all experiments at different temperature, pressure and CO 2 concentrations. Shear viscosities of PS as well as PS/CO 2 were described using the generalized Cross-Carreau model and the Doolittle equation and different free volume models were compared.
Effect of the economic crisis on the use of health and home care services among Spanish COPD patients

Background Chronic obstructive pulmonary disease (COPD) is a major cause of disability and death worldwide. Consequently, COPD patients are frequent users of health and social resources. Therefore, they are highly vulnerable to decreases in investment in healthcare services. We aimed to describe the utilization of health and home care services among Spanish COPD patients during the economic crisis to identify factors independently associated with changes in the utilization of these services and to study the time trends from 2009 to 2014. Methods We used data from the European Health Interview Surveys for Spain (EHSS) conducted between 2009/2010 (n=22,188) and 2014 (n=22,842). We included responses from adults with COPD aged 40 years or over. Dependent variables included self-reported hospitalizations during the previous year, general practitioner (GP) visits during the last 4 weeks, other health care services used during the previous year (nursing, rehabilitation, and psychological services), and home care services use during the previous year. Independent variables included demographic and socioeconomic characteristics, health status variables, and lifestyles. Results We identified 1,328 and 1,008 COPD patients from EHSS 2009 and EHSS 2014, respectively. We observed a significant increase in non-GP services use (30.6% in 2009 vs 39.11% in 2014; p<0.001). No changes were found for hospitalizations, GP visits, and home care services use over time. Multivariable models showed that associated factors with a higher use included any chronic comorbidity and worse self-rated health. Physical activity was a strong predictor of fewer hospitalizations and less home care service use. Female sex was associated with significantly fewer hospitalizations (OR 0.72; 95% CI 0.58–0.89). Conclusion We found an increase in the use of non-GP services (nursing, rehabilitation, and psychological) but not in other health and home care services. The only differences in hospitalizations were observed according to sex. Therefore, the effect of the economic crisis, if any, seems to have been of small magnitude.
A Unified Approach for the H∞-Stability Analysis of Classical and Fractional Neutral Systems with Commensurate Delays

We examine the stability of linear integer-order and fractional-order systems with commensurate delays of neutral type in the sense of $H_\infty$-stability. The systems may have chains of poles approaching the imaginary axis. While several classes of these systems have been previously studied on a case-by-case basis, a unified method is proposed in this paper which allows one to deal with all these classes at the same time. Approximation of poles of large modulus is systematically calculated based on a convex hull derived from the coefficients of the system. This convex hull also serves to establish sufficient conditions for instability and necessary and sufficient conditions for stability.
Basic Composition and Enriched Integration in Idiom Processing: An EEG Study

We investigated the extent to which the literal meanings of the words forming literally plausible idioms (e.g., break the ice) are semantically composed and how the idiomatic meaning is integrated in the unfolding sentence representation. Participants read ambiguous idiom strings embedded in highly predictable, literal, and idiomatic contexts while their EEG was recorded. Control sentences only contained the idiom-final word whose cloze values were as high as in literal and idiomatic contexts. Event-related potentials data showed that differences in the amplitude of a frontal positivity (PNP) emerged at the beginning and at the end of the idiom strings, with the idiomatic context condition associated with more positive voltages. The time frequency analysis of the EEG showed an increase in power of the middle gamma frequency band only in the literal context condition. These findings suggest that sentence revision mechanisms, associated with the frontal PNP, are involved in idiom meaning integration, and that the literal semantic composition of the idiomatic constituents, associated with changes in gamma frequency, is not carried out after idiom recognition.
Gab2 mediates hepatocellular carcinogenesis by integrating multiple signaling pathways

Our previous studies have found that Growth factor receptor‐bound protein 2–associated binding protein 2 (Gab2)—a docking protein—governs the development of fatty liver disease. Here, we further demonstrate that Gab2 mediates hepatocarcinogenesis. Compared with a faint expression in para‐carcinoma tissue, Gab2 was highly expressed in ~60–70% of human hepatocellular carcinoma (HCC) specimens. Deletion of Gab2 dramatically suppressed diethylnitrosamine‐induced HCC in mice. The oncogenic effects of Gab2 in HepG2 cells were promoted by Gab2 overexpression but were rescued by Gab2 knockdown. Furthermore, Gab2 knockout in HepG2 cells restrained cell proliferation, migration and tumor growth in nude mice. Signaling pathway analysis with protein kinase inhibitors demonstrated that oncogenic regulation by Gab2 in hepatic cells involved multiple signaling molecules, including ERK, Akt, and Janus kinases (Jaks), especially those that mediate inflammatory signaling. IL‐6 signaling was increased by Gab2 overexpression and impaired by Gab2 deletion via regulation of Jak2 and signal transducer and activator of transcription 3 phosphorylation and the expression of downstream genes, such as Bcl‐2 (B‐cell lymphoma 2), c‐Myc, MMP7 (matrix metalloproteinase‐7), and cyclin D1 in vitro and in vivo. These data indicate that Gab2 mediates the pathologic progression of HCC by integrating multiple signaling pathways and suggest that Gab2 might be a powerful therapeutic target for HCC. —Cheng, J., Zhong, Y. , Chen, S. , Sun, Y. , Huang, L. , Kang, Y. , Chen, B. , Chen, G. , Wang, F. , Tian, Y. , Liu, W. , Feng, G. ‐S. , Lu, Z. Gab2 mediates hepatocellular carcinogenesis by integrating multiple signaling pathways. FASEB J. 31, 5530–5542 (2017). www.fasebj. org