Miracle-dz/UniFAR-FTUs huggingface dataset:
Median nerve behavior at different wrist positions among older males

The effect of wrist flexion-extension on the median nerve appearance, namely the cross-sectional area (MNCSA) and the longitudinal (D1) and vertical (D2) diameters, was investigated among older adults (N = 34). Ultrasound examination was conducted to examine the median nerve at different wrist angles (neutral; and 15°, 30°, and 45° extension and flexion), in both the dominant and nondominant hand. Median nerve behavior were significantly associated with wrist angle changes. The MNCSA at wrist flexion and extension were significantly smaller (P < .001) compared with the neutral position in both the dominant and nondominant hand. The D1 and D2 were significantly reduced at flexion (P < .001) and extension (P < .001), respectively, in both the dominant and nondominant hand. Our results suggest that a larger flexion-extension angle causes higher compression stress on the median nerve, leading to increased deformation of the MNCSA, D1, and D2 among older adults.
A High Efficiency and Low Ripple Cross-Coupled Charge Pump Circuit

Abstract: A fully integrated cross-coupled charge pump circuit with four-clock signals and a new method of body bias have been proposed. The new clock scheme eliminates all of the reversion power loss and reduces the ripple voltage. In addition, the largest voltage differences between the terminals of all transistors do not exceed the supply voltage. We have also solved the gate-oxide overstress problem in the conventional charge pump circuits and enhanced the reliability. The proposed charge pump circuit has been simulated using Spectre and in the TSMC 0.18um CMOS process. The simulation results show that the maximum voltage conversion efficiency of the new 3-stage cross-coupled circuit with an input voltage of 1.5V is 99.8%. Moreover, the output ripple voltage has been significantly reduced.
The relationship between chronic whiplash-associated disorder and post-traumatic stress: attachment-anxiety may be a vulnerability factor

Background: In more than 90% of whiplash accidents a good explanation regarding the association between trauma mechanism, organic pathology, and persistent symptoms has failed to be provided. Objective: We predicted that the severity of chronic whiplash-associated disorder (WAD), measured as number of whiplash symptoms, pain duration, pain-related disability, and degree of somatisation would be associated with the number of post-traumatic stress disorder symptoms (PTSD). Secondly, we expected attachment-anxiety to be a vulnerability factor in relation to both PTSD and WAD. Design: Data were collected from 1,349 women and 360 men suffering from WAD from the Danish Society for Polio, Traffic, and Accident Victims. The PTSD symptoms were measured by the Harvard Trauma Questionnaire. All three core PTSD clusters were included: re-experiencing, avoidance, and hyperarousal. Attachment security was measured along the two dimensions, attachment-anxiety and attachment-avoidance, by the Revised Adult Attachment Scale. Results: PTSD symptoms were significantly related to the severity of WAD. In particular, the PTSD clusters of avoidance and hyperarousal were associated with the number of whiplash symptoms, disability, and somatisation. Attachment-anxiety was significantly related to PTSD symptoms and somatisation but not to pain and disability. A co-morbidity of 38.8% was found between the PTSD diagnosis and WAD, and about 20% of the sample could be characterised as securely attached. Conclusions: The PTSD clusters of avoidance and hyperarousal were significantly associated with severity of WAD. The study emphasises the importance of assessing PTSD symptomatology after whiplash injury. Furthermore, it highlights that attachment theory may facilitate the understanding of why some people are more prone to develop PTSD and WAD than others. For abstract or full text in other languages, please see Supplementary files under Reading Tools online
The Incidence and Types of Physical Contact Associated with Body Checking Regulation Experience in 13–14 Year Old Ice Hockey Players

Background: Ice hockey has one of the highest sport participation and injury rates in youth in Canada. Body checking (BC) is the predominant mechanism of injury in leagues in which it is permitted. The objectives of this study were to determine whether the incidence and types of physical contact differ for Bantam players (aged 13–14 years) who were exposed to BC at Pee Wee level (aged 11–12 years) in Calgary, Alberta versus Bantam players who were not exposed to BC at Pee Wee level in Québec City, Québec. All teams were exposed to BC at bantam level; Methods: A cohort study was conducted in Québec City and Calgary. Sixteen games for Calgary and 15 for Québec City were randomly selected and analysed with a validated observation system to quantify five intensities of physical contact and to observe different types of physical contact such as slashing and holding; Results: A total of 5610 incidences of physical contact with the trunk and 3429 other types of physical contact were observed. Very light intensity trunk contact was more frequent in Calgary (adjusted incidence RR (ARR): 1.71; 95% CI: 1.28–2.29). Holding (ARR: 1.04; 95% CI: 1.02–1.07) and slashing (ARR: 1.38; 95% CI: 1.07–1.77) were more frequent in Calgary; Conclusion: Results suggest that players’ physical contacts differ between Bantam leagues in which BC was permitted at Pee Wee level and leagues in which it was not permitted until Bantam level.
Pharyngeal cyst arising from second branchial cleft

Abstract A rare case of pharyngeal cyst arising from the second branchial cleft in a 14-year-old boy is described. A cyst located in the right posterolateral wall of the oropharynx was completely removed by an intraoral approach. Histopathological examination revealed that the cyst was lined with columnar (respiratory type) epithelium.
Participation of the Arabidopsis bHLH Factor GL3 in Trichome Initiation Regulatory Events1[W][OA]

The development of trichomes (leaf hairs) from pluripotent epidermal cells in Arabidopsis (Arabidopsis thaliana) provides a powerful system to investigate the regulatory motifs involved in plant cell differentiation. We show here that trichome initiation is triggered within 4 h of the induction of the GLABRA3 (GL3) basic helix-loop-helix transcription factor. Within this developmental window, GL3 binds to the promoters of at least three genes previously implicated in the development and patterning of trichomes (GL2, CAPRICE, and ENHANCER OF TRIPTYCHON AND CAPRICE1) and activates their transcription. The in vivo binding of GL3 to the promoters of these genes requires the presence of the R2R3-MYB factor GL1, supporting a model in which a GL3-GL1 complex is part of the trichome initiation enhanceosome. In contrast, GL3 is recruited to its own promoter in a GL1-independent manner, and this results in decreased GL3 expression, suggesting the presence of a GL3 negative autoregulatory loop. In support of genetic analyses indicating that ENHANCER OF GL3 (EGL3) is partially redundant with GL3, we show that EGL3 shares some direct targets with GL3. However, our results suggest that GL3 and EGL3 work independently of each other. Taken together, our results provide a regulatory framework to understand early events of epidermal cell differentiation.
In Silico Sequence Analysis Reveals New Characteristics of Fungal NADPH Oxidase Genes

Abstract NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferricchelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bioinformatic approaches used to identify Nox-encoding genes. Further, most studies on fungal Nox genes have focused mainly on functionality, rather than sequence properties, and consequently clear differentiation among the various Nox isoforms has not been achieved. We conducted an extensive sequence analysis to identify putative Nox genes among 34 eukaryotes, including 28 fungal genomes and one Oomycota genome. Analyses were performed with respect to phylogeny, transmembrane helices, di-histidine distance and glycosylation. Our analyses indicate that the sequence properties of fungal Nox genes are different from those of human and plant Nox genes, thus providing novel insight that will enable more accurate identification and characterization of fungal Nox genes.
Efficient Approximation Algorithms for Strings Kernel Based Sequence Classification

Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the two sequences. Extending this definition, by considering two $k$-mers to match if their distance is at most $m$, yields better classification performance. This, however, makes the problem computationally much more complex. Known algorithms to compute this similarity have computational complexity that render them applicable only for small values of $k$ and $m$. In this work, we develop novel techniques to efficiently and accurately estimate the pairwise similarity score, which enables us to use much larger values of $k$ and $m$, and get higher predictive accuracy. This opens up a broad avenue of applying this classification approach to audio, images, and text sequences. Our algorithm achieves excellent approximation performance with theoretical guarantees. In the process we solve an open combinatorial problem, which was posed as a major hindrance to the scalability of existing solutions. We give analytical bounds on quality and runtime of our algorithm and report its empirical performance on real world biological and music sequences datasets.
A High-Throughput Method for Illumina RNA-Seq Library Preparation

With the introduction of cost effective, rapid, and superior quality next generation sequencing techniques, gene expression analysis has become viable for labs conducting small projects as well as large-scale gene expression analysis experiments. However, the available protocols for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput applications. Also, most protocols require isolated total RNA as a starting point. We provide a cost-effective RNA-Seq library synthesis protocol that is fast, starts with tissue, and is high-throughput from tissue to synthesized library. We have also designed and report a set of 96 unique barcodes for library adapters that are amenable to high-throughput sequencing by a large combination of multiplexing strategies. Our developed protocol has more power to detect differentially expressed genes when compared to the standard Illumina protocol, probably owing to less technical variation amongst replicates. We also address the problem of gene-length biases affecting differential gene expression calls and demonstrate that such biases can be efficiently minimized during mRNA isolation for library preparation.
Analysis of Human APOBEC3H Haplotypes and Anti-Human Immunodeficiency Virus Type 1 Activity

ABSTRACT Human APOBEC3H (A3H) has one cytidine deaminase domain (CDD) and inhibits the replication of retrotransposons and human immunodeficiency virus type 1 (HIV-1) in a Vif-resistant manner. Human A3H has five single amino acid polymorphisms (N15Δ, R18L, G105R, K121D, and E178D), and four haplotypes (I to IV) have previously been identified in various human populations. Haplotype II was primarily found in African-derived populations, and it was the only one that could be stably expressed. Here, we identified three new haplotypes from six human population samples, which we have named V, VI, and VII. Haplotypes V and VII are stably expressed and inhibit HIV-1 replication. Notably, haplotype V was identified in samples from all African-, Asian-, and Caucasian-derived populations studied. Using haplotype VII, we investigated the A3H anti-HIV-1 mechanism. We found that A3H virion packaging is independent of its CDD but dependent on a 112YYXW115 motif. This motif binds HIV-1 nucleocapsid in an RNA-dependent manner, and a single Y112A mutation completely disrupts A3H virion incorporation. We further studied the mechanism of A3H resistance to Vif. Although the previously identified APOBEC3G Vif-responsive motif 128DPDY131 is not conserved in A3H, placement of this motif into A3H does not make it become less resistant to HIV-1 Vif. We conclude that stably expressed A3H haplotypes may be more broadly distributed in humans than previously realized, and A3H protein is resistant to Vif. These results have important implications for the role of A3H in retrotransposon and HIV-1 inhibition.
Comparison of the Effects of Heparin and 0.9% Sodium Chloride Solutions in Maintenance of Patency of Central Venous Catheters

Background Occlusion of central venous catheters is one of the limiting factors in using them. Heparinized saline solution is the standard solution used for keeping the catheters open. Objectives This study aimed to determine the effect of heparin saline solution and normal saline in maintenance of patency of central venous catheters. Patients and Methods This double-blind study was performed on 84 patients of intensive care unit who had central venous catheters. The patients were randomly divided into two groups of heparin saline receivers and normal saline receivers. In the heparin group after each drug injection into the lumen, 3 mL of heparin saline solution was injected in the catheter as well. The other group only received 10 mL of normal saline instead. The catheters were examined for blood return and flushing every eight hours for 21 days. Data was analyzed using SPSS software version 20 and descriptive and analytic statistics were studied. Results There was no significant difference in the rate of flushing (P = 0.872) and possibility of taking blood samples from catheters (P = 0.745) in the two groups of heparin and normal saline receivers. Furthermore, using heparin had no effect on prolonging the survival of catheters. Conclusions Considering possible side effects of heparin and the increase in treatment charges and the fact that using heparin did not have a significant effect on patency and survival of catheters in the studied patients, it is recommended to use normal saline solution to maintain the patency of central venous catheters.
Role Transfer Problems and Algorithms

Role transfer is a usual activity in an organization, particularly in a crisis situation. Role assignment and transfer regulations are important to accomplish it. This paper discusses the general role transfer problem; proposes a role specification mechanism; builds a set of terminologies for role transfer based on a revised environment-class, agent, role, group, and object model; and presents algorithms to validate role transfer while maintaining group viability. The contributions include formulating the problem of role transfer in a generalized form, developing a set of algorithms, and presenting a solution when group members are insufficient.
Natural-Gradient Stochastic Variational Inference for Non-Conjugate Structured Variational Autoencoder

We propose a new method for amortized inference in graphical models that contain deep generative models. Our method generalizes existing approaches to a larger class of models where the graphical model can contain non-conjugate components. Our main contribution is the proposal of structured recognition models that preserve the correlations between all local variables. For this general class of models, we derive a scalable inference method that employs natural-gradient updates and can be implemented by reusing existing software for graphical models and deep models.
Evaluation of direct immunofluorescence test for diagnosis of upper respiratory tract infection by Chlamydia pneumoniae.

BACKGROUND Chlamydia pneumoniae causes a variety of respiratory infections and is involved in cardiovascular diseases. Diagnosis of C. pneumoniae infection currently relies on antibody detection by microimmunofluorescence (MIF), which has limited use, and is the retrospective diagnosis for acute infection. OBJECTIVE Find an effective early diagnosis of acute upper respiratory infection, or use in combination with MIF to accurately diagnose the infection by C. pneumoniae. MATERIAL AND METHOD Direct immunofluorescence (DIF) was developed to detect C. pneumoniae in nasopharyngeal specimens obtained from patients with upper respiratory tract infection, and normal individuals. IgM and IgG antibodies against C. pneumoniae by MIF were determined for evaluation of the detected C. pneumoniae and seroconversion. RESULTS DIF gave positive results in 29 of 37 (78.4%) samples from 31 patients. Fifteen samples positive by DIF illustrated antibody titers interpreted as acute C. pneumoniae infection, and eight DIF positive samples showed antibody titers of chronic infection. Negative results by both DIF and MIF were found in two patients and 23 of 25 by DIF but 20 of 25 by MIF in normal subjects. Five paired sera subsequently collected from three of the 31 patients illustrated seroconversion 2-4 months after the primary specimen collection, which gave positive results by DIF but negative for antibodies. Significant association was found between C. pneumoniae detection by DIF and antibodies by MIF when analysis was done in the group of patients and normal subjects (p < 0.001; Pearson chi-square test). CONCLUSION DIF could be an alternative assay for early diagnosis of C. pneumoniae infection, and may be used in combination with MIF for accurate diagnosis of acute C. pneumoniae infection.
Sharpness of Spike Initiation in Neurons Explained by Compartmentalization

In cortical neurons, spikes are initiated in the axon initial segment. Seen at the soma, they appear surprisingly sharp. A standard explanation is that the current coming from the axon becomes sharp as the spike is actively backpropagated to the soma. However, sharp initiation of spikes is also seen in the input–output properties of neurons, and not only in the somatic shape of spikes; for example, cortical neurons can transmit high frequency signals. An alternative hypothesis is that Na channels cooperate, but it is not currently supported by direct experimental evidence. I propose a simple explanation based on the compartmentalization of spike initiation. When Na channels are placed in the axon, the soma acts as a current sink for the Na current. I show that there is a critical distance to the soma above which an instability occurs, so that Na channels open abruptly rather than gradually as a function of somatic voltage.
RC3E: Provision and Management of Reconfigurable Hardware Accelerators in a Cloud Environment

Heterogeneous systems consisting of general-purpose processors and different types of hardware accelerators are becoming more and more common in HPC systems. Especially FPGAs provide a promising opportunity to improve both performance and energy efficiency of such systems. Adding FPGAs to clouds or data centers allows easy access to such reconfigurable resources. In this paper we present our cloud service models and cloud hypervisor called RC3E, which integrates virtualized FPGA-based hardware accelerators into a cloud environment. With our hardware and software framework, multiple (virtual) user designs can be executed on a single physical FPGA device. We demonstrate the performance of our approach by implementing up to four virtual user cores on a single device and present future perspectives for FPGAs in cloud-based data environments.
Bone Marrow Stromal Cells Promote Neurite Extension in Organotypic Spinal Cord Slice: Significance for Cell Transplantation Therapy

Objective. Recent reports have indicated that bone marrow stromal cells (BMSCs) have the potential to improve neurological function when transplanted into models of central nervous system (CNS) disorders, including traumatic spinal cord injury. In this study, the authors aimed to clarify the underlying mechanism through which BMSCs supported CNS regeneration in the spinal cord. Methods. The authors topically applied mouse BMSCs expressing green fluorescence protein (0.4-4 × 104 cells) on the organotypic spinal cord slice culture prepared from 6-day-old rat pups (n = 17). They were co-cultured for 3 weeks after the slice culture started, and the behavior of the applied BMSCs was serially observed using a fluorescence bioimaging technique. The authors completed a histological analysis at the end of the co-cultures and evaluated the profiles of the cultured BMSCs using microarray and immunocytochemistry techniques. Results. The fluorescence bioimaging showed that the BMSCs survived and made a cluster on the slice during the experiments. They also induced a morphological change in the slice within 48 hours of co-culture. Immunohistochemistry analysis showed that the BMSCs promoted a marked neurite extension toward their cluster and some of the BMSCs expressed Tuj-1, an early neuronal marker. Analysis by microarray and immunocytochemistry revealed that BMSCs highly expressed the matrix metalloproteinases (MMPs), stromal cell—derived factor-1, and its specific receptor CXCR4. Conclusions . These findings suggest that the donor BMSCs can support CNS regeneration due to their acquisition of a suitable environment for differentiation and promotion of neurite extension via MMPs and chemokines.
Preoperative Cognitive Stratification of Older Elective Surgical Patients: A Cross-Sectional Study

BACKGROUND:Preexisting cognitive impairment is emerging as a predictor of poor postoperative outcomes in seniors. We hypothesized that preoperative cognitive screening can be performed in a busy preadmission evaluation center and that cognitive impairment is prevalent in elective geriatric surgical patients. METHODS:We approached 311 patients aged 65 years and older presenting for preoperative evaluation before elective surgery in a prospective, observational, single-center study. Forty-eight patients were ineligible, and 63 declined. The remaining 200 were randomly assigned to the Mini-Cog (N =100) or Clock-in-the-Box [CIB; N = 100)] test. Study staff administered the test in a quiet room, and 2 investigators scored the tests independently. Probable cognitive impairment was defined as a Mini-Cog ⩽ 2 or a CIB ⩽ 5. RESULTS:The age of consenting patients was 73.7 ± 6.4 (mean ± SD) years. There were no significant differences between patients randomly assigned to the Mini-Cog and CIB test in age, weight, gender, education, ASA physical status, or Charlston Index. Overall, 23% of patients met criteria for probable cognitive impairment, and prevalence was virtually identical regardless of the test used; 22% screened with the Mini-Cog and 23% screened with the CIB scored as having probable cognitive impairment (P = 1.0 by &khgr;2 analysis). Both tests had good interrater reliability (Krippendroff &agr; = 0.86 [0.72–0.93] for Mini-Cog and 11 for CIB). CONCLUSIONS:Preoperative cognitive screening is feasible in most geriatric elective surgical patients and reveals a substantial prevalence of probable cognitive impairment in this population.