Miracle-dz/UniFAR-FTUs huggingface dataset:
VGLUT1 synapses and P‐boutons on regenerating motoneurons after nerve crush

Stretch‐sensitive Ia afferent monosynaptic connections with motoneurons form the stretch reflex circuit. After nerve transection, Ia afferent synapses and stretch reflexes are permanently lost, even after regeneration and reinnervation of muscle by motor and sensory afferents is completed in the periphery. This loss greatly affects full recovery of motor function. However, after nerve crush, reflex muscle forces during stretch do recover after muscle reinnervation and reportedly exceed 140% baseline values. This difference might be explained by structural preservation after crush of Ia afferent synapses on regenerating motoneurons and decreased presynaptic inhibitory control. We tested these possibilities in rats after crushing the tibial nerve (TN), and using Vesicular GLUtamate Transporter 1 (VGLUT1) and the 65 kDa isoform of glutamic acid‐decarboxylase (GAD65) as markers of, respectively, Ia afferent synapses and presynaptic inhibition (P‐boutons) on retrogradely labeled motoneurons. We analyzed motoneurons during regeneration (21 days post crush) and after they reinnervate muscle (3 months). The results demonstrate a significant loss of VGLUT1 terminals on dendrites and cell bodies at both 21 days and 3 months post‐crush. However, in both cellular compartments, the reductions were small compared to those observed after TN full transection. In addition, we found a significant decrease in the number of GAD65 P‐boutons per VGLUT1 terminal and their coverage of VGLUT1 boutons. The results support the hypothesis that better preservation of Ia afferent synapses and a change in presynaptic inhibition could contribute to maintain or even increase the stretch reflex after nerve crush and by difference to nerve transection.
Short Term Effects on Bone Quality Associated with Consumption of Soy Protein Isolate and Other Dietary Protein Sources in Rapidly Growing Female Rats

Beneficial effects of soy protein consumption on bone quality have been reported. The effects of other dietary protein sources such as whey protein hydrolysate (WPH) and rice protein isolate (RPI) on bone growth have been less well examined. The current study compared effects of feeding soy protein isolate (SPI), WPH and RPI for 14 d on tibial bone mineral density (BMD) and bone mineral content (BMC) in intact and ovariectomized (OVX) rapidly growing female rats relative to animals fed casein (CAS). The effects of estrogenic status on responses to SPI were also explored. Tibial peripheral quantitative computerized tomography (pQCT) showed all three protein sources had positive effects on either BMD or BMC relative to CAS (P < 0.05), but SPI had greater effects in both intact and OVX female rats. SPI and E2 had positive effects on BMD and BMC in OVX rats (P < 0.05). However, trabecular BMD was lower in a SPI + E2 group compared to a CAS + E2 group. In OVX rats, SPI increased serum bone formation markers, and serum from SPI-fed rats stimulated osteoblastogenesis in ex vivo. SPI also suppressed the bone resorption marker RatLaps (P < 0.05). Both SPI and E2 increased alkaline phosphatase gene expression in bone, but only SPI decreased receptor activator of nuclear factor-κB ligand (RANKL) and estrogen receptor gene expression (P < 0.05). These data suggest beneficial bone effects of a soy diet in rapidly growing animals and the potential for early soy consumption to increase peak bone mass.
Review: Rapid virological response to peginterferon alfa and ribavirin treatment of chronic hepatitis C predicts sustained virological response and relapse in genotype 1 patients

The treatment of chronic hepatitis C is a rapidly changing arena with new medications, new guidelines, and an evolving understanding of the virus, host factors and natural history. With the explosion of new information, the educational infrastructure to update clinicians has been outpaced; many feel uncertain if the tools they are using to care for patients are meeting the standard of practice. This review focuses on the most common genotype of the hepatitis C virus and the rules of engagement when treating with pegylated interferon and ribavirin. Viral assessment guideposts are evaluated and put into context for a clinical audience. The expected arrival of newer antiviral therapies is still years away, and maximizing the current treatment regimens is of utmost importance to eradicate virus when feasible, while minimizing toxicity.
Palliative Care Planner: A Pilot Study to Evaluate Acceptability and Usability of an Electronic Health Records System‐integrated, Needs‐targeted App Platform

Rationale: The quality and patient‐centeredness of intensive care unit (ICU)‐based palliative care delivery is highly variable. Objective: To develop and pilot an app platform for clinicians and ICU patients and their family members that enhances the delivery of needs‐targeted palliative care. Methods: In the development phase of the study, we developed an electronic health record (EHR) system‐integrated mobile web app system prototype, PCplanner (Palliative Care Planner). PCplanner screens the EHR for ICU patients meeting any of five prompts (triggers) for palliative care consultation, allows families to report their unmet palliative care needs, and alerts clinicians to these needs. The evaluation phase included a prospective before/after study conducted at a large academic medical center. Two control populations were enrolled in the before period to serve as context for the intervention. First, 25 ICU patients who received palliative care consults served as patient‐level controls. Second, 49 family members of ICU patients who received mechanical ventilation for at least 48 hours served as family‐level controls. Afterward, 14 patients, 18 family members, and 10 clinicians participated in the intervention evaluation period. Family member outcomes measured at baseline and 4 days later included acceptability (Client Satisfaction Questionnaire [CSQ]), usability (Systems Usability Scale [SUS]), and palliative care needs, assessed with the adapted needs of social nature, existential concerns, symptoms, and therapeutic interaction (NEST) scale; the Patient‐Centeredness of Care Scale (PCCS); and the Perceived Stress Scale (PSS). Patient outcomes included frequency of goal concordant treatment, hospital length of stay, and discharge disposition. Results: Family members reported high PCplanner acceptability (mean CSQ, 14.1 [SD, 1.4]) and usability (mean SUS, 21.1 [SD, 1.7]). PCplanner family member recipients experienced a 12.7‐unit reduction in NEST score compared with a 3.4‐unit increase among controls (P = 0.002), as well as improved mean scores on the PCCS (6.6 [SD, 5.8]) and the PSS (−0.8 [SD, 1.9]). The frequency of goal‐concordant treatment increased over the course of the intervention (n = 14 [SD, 79%] vs. n = 18 [SD, 100%]). Compared with palliative care controls, intervention patients received palliative care consultation sooner (3.9 [SD, 2.7] vs. 6.9 [SD, 7.1] mean days), had a shorter mean hospital length of stay (20.5 [SD, 9.1] vs. 22.3 [SD, 16.0] patient number), and received hospice care more frequently (5 [36%] vs. 5 [20%]), although these differences were not statistically significant. Conclusions: PCplanner represents an acceptable, usable, and clinically promising systems‐based approach to delivering EHR‐triggered, needs‐targeted ICU‐based palliative care within a standard clinical workflow. A clinical trial in a larger population is needed to evaluate its efficacy.
Sema3A Reduces Sprouting of Adult Rod Photoreceptors In Vitro

Purpose Rod photoreceptor terminals respond to retinal injury with retraction and sprouting. Since the guidance cue Semaphorin3A (Sema3A) is observed in the retina after injury, we asked whether Sema3A contributes to structural plasticity in rod photoreceptors. Methods We used Western blots and alkaline phosphatase (AP)-tagged neuropilin-1 (NPN-1) to detect the expression of Sema3A in an organotypic model of porcine retinal detachment. We then examined Sema3A binding to cultured salamander rod photoreceptors using AP-tagged Sema3A. For functional analysis, we used a microspritzer to apply a gradient of Sema3A-Fc to isolated salamander rod photoreceptors over 24 hours. Results Sema3A protein was biochemically detected in porcine retinal explants in the retina 7, 24, and 72 hours after detachment. In sections, NPN-1 receptor was bound to the inner and outer retina. For isolated rod photoreceptors, Sema3A localized to synaptic terminals and to neuritic processes after 1 week in vitro. In microspritzed rod photoreceptors, process initiation occurred away from high concentrations of Sema3A. Sema3A significantly decreased the number of processes formed by rod photoreceptors although the average length of processes was not affected. The cellular orientation of rod photoreceptors relative to the microspritzer also significantly changed over time; this effect was reduced with the Sema3A inhibitor, xanthofulvin. Conclusion Sema3A is expressed in the retina after detachment, binds to rod photoreceptors, affects cell orientation, and reduces photoreceptor process initiation in vitro. Our results suggest that Sema3A contributes to axonal retraction in retinal injury, whereas rod neuritic sprouting and regenerative synaptogenesis may require a reduction in semaphorin signaling.
CNNs with cross-correlation matching for face recognition in video surveillance using a single training sample per person

In video surveillance, face recognition (FR) systems seek to detect individuals of interest appearing over a distributed network of cameras. Still-to-video FR systems match faces captured in videos under challenging conditions against facial models, often designed using one reference still per individual. Although CNNs can achieve among the highest levels of accuracy in many real-world FR applications, state-of-the-art CNNs that are suitable for still-to-video FR, like trunk-branch ensemble (TBE) CNNs, represent complex solutions for real-time applications. In this paper, an efficient CNN architecture is proposed for accurate still-to-video FR from a single reference still. The CCM-CNN is based on new cross-correlation matching (CCM) and triplet-loss optimization methods that provide discriminant face representations. The matching pipeline exploits a matrix Hadamard product followed by a fully connected layer inspired by adaptive weighted cross-correlation. A triplet-based training approach is proposed to optimize the CCM-CNN parameters such that the inter-class variations are increased, while enhancing robustness to intra-class variations. To further improve robustness, the network is fine-tuned using synthetically-generated faces based on still and videos of non-target individuals. Experiments on videos from the COX Face and Chokepoint datasets indicate that the CCM-CNN can achieve a high level of accuracy that is comparable to TBE-CNN and HaarNet, but with a significantly lower time and memory complexity. It may therefore represent the better trade-off between accuracy and complexity for real-time video surveillance applications.
A study of fair usage policy effects on VoIP quality from social networking applications

This paper presents a study of VoIP quality from social networking applications over 3G with Fair Usage Policy (FUP) using stationary tests. It has been found that VoIP quality over 3G with FUP from the same VoIP applications tend to provide lower VoIP quality than over 3G with Access Unlimited Internet Service (AUIS), particularly Skype provides lower VoIP quality obviously. Also it has been found that over 3G with FUP provided by one operator, LINE tends to provide better VoIP quality than Skype and Tango although there is no significant difference (p-value > 0.05), while OOVOO provides the lowest VoIP quality.
Differential evolution-binary particle swarm optimization algorithm for the analysis of aryl β-diketo acids for HIV-1 integrase inhibition

A hybrid differential evolution-binary particle swarm optimization (DE-BPSO) algorithm is proposed as a feature selection algorithm in the development of quantitative structure-activity relationship (QSAR) models. DE is used to evolve the velocities of the particle swarm from which a series of rules are used to determine the discrete values of the position vectors which form chemical descriptor subsets. These descriptor subsets are then used to develop models for QSAR analysis. DE-BPSO was found to outperform the standalone BPSO algorithm. The DE-BPSO algorithm was then used to develop multiple linear regression models for the analysis of aryl β-diketo acid compounds for the inhibition of HIV-1 integrase. This model highlights the significance of hydrophobicity and partial positive charges of the hydrogen atoms on the molecular surface in influencing the biological activities of these compounds for the inhibition of HIV-1 integrase.
How can we get benefits of computer‐based testing in engineering education?

Using computers for assessment can provide several benefits for educators and test‐takers. However, in the literature, there is no consensus on the equivalence of paper‐and‐pencil (P&P) and computer‐based test (CBT) environments. Additionally, these studies fail to address the engineering domain. Our main assumption is that, if we could define the confounding factors to satisfy that these two versions of the tests provide equivalent results, then especially in the first year courses of the engineering education programs, we could get several benefits of the CBT environments. Accordingly, in this study, students' performance on different test modes was evaluated on 209 first year engineering students of a chemistry course. The results of this study showed that there is no significant performance difference between P&P and CBT. By comparing results with the previous studies, this study concludes that personal characteristics of test takers, the features of CBT systems, and the test content are all possible confounding factors when comparing test modes and need to be considered by the implementers. The results of this study show that once these factors are controlled, students' performance on CBTs and P&P tests in chemistry courses will not vary. This finding is encouraging the educators to get benefits of CBTs without any affect on students' performance. © 2010 Wiley Periodicals, Inc. Comput Appl Eng Educ 21: 287–293, 2013
Recent Trends in Deep Learning Based Natural Language Processing

Deep learning methods employ multiple processing layers to learn hierarchical representations of data and have produced state-of-the-art results in many domains. Recently, a variety of model designs and methods have blossomed in the context of natural language processing (NLP). In this paper, we review significant deep learning related models and methods that have been employed for numerous NLP tasks and provide a walk-through of their evolution. We also summarize, compare and contrast the various models and put forward a detailed understanding of the past, present and future of deep learning in NLP.
Diagnostic and prognostic value of miR-106a in colorectal cancer

We sought to systematically evaluate the diagnostic and prognostic value miR106a in patients with colorectal cancer (CRC). An original study was conducted to explore correlations between tissue miR106a levels and outcomes for 138 patients diagnosed with CRC. To explore the diagnostic performance of miR106a, eligible studies were identified from medical databases from China and abroad. Based on these results, 15 studies (including our original study) were pooled and included in a meta-analyses. The pooled sensitivity, specificity, and diagnostic odds ratios of miR106a were 0.53 (95% confidence interval (CI): 0.49–0.57), 0.85 (95% CI: 0.82–0.88), and 7.22 (95% CI: 3.17–16.44) for diagnosis of CRC, and the area under the curve (AUC) for miR106a when diagnosing CRC was 0.72. Patients with higher expression of tissue miR106a had poor overall survival (pooled hazard ratio (HR): 1.50; 95% CI: 1.02–2.20), but not disease-free survival (pooled HR: 1.03; 95% CI: 0.40–2.65). Overexpression of miR106a may predict superior metastasis-free survival (pooled HR: 0.65; 95% CI: 0.33–1.27), but the effect was not significant in this study (p = 0.21).
Secretion of interleukin-6 by bone marrow mesenchymal stem cells promotes metastasis in hepatocellular carcinoma

Mesenchymal stem cells (MSCs) interact with tumor cells and regulate tumorigenesis and metastasis. As one of the important components of the tumor microenvironment, MSC-secreted cytokines play a critical role in cancer development. However, whether and how bone marrow MSCs (BMSCs) and their secreted cytokines participate in hepatocellular carcinoma (HCC) progression, still remains largely unknown. In the present study, we first measured the concentration of interleukin-6 (IL-6) in BMSC conditioned medium (BMSC-CM). Next, we assessed the changes of invasion ability in response to treatment of BMSC-CM or recombinant IL-6 in two human HCC cell lines Bel-7404 and HepG2. Then we analyzed the level of key components of the IL-6 signal pathway, including IL-6 receptor and signal transducer (i.e. IL-6R and gp130), a transcription factor STAT3 (signal transducer and activator of transcription 3), as well as its target genes BCL2, CCND1, MCL1 and MMP2, in BMSC-CM or recombinant IL-6 treated Bel-7404 and HepG2 cells. Results showed that a considerable amount of IL-6 was secreted by BMSCs, and BMSC-CM markedly elevated Bel-7404 cell invasion rate and stimulated the signal transduction of IL-6/STAT3 pathway. Neutralizing the secreted IL-6 bioactivity by the anti-IL-6 antibody diminished the invasion-promoting effect and down-regulated IL-6/STAT3 pathway of BMSC-CM treated Bel-7404 cells. In conclusion, we found that BMSCs may activate the IL-6/STAT3 signaling pathway and promote cell invasion in Bel-7404 cells, suggesting that this protumor effect should be seriously considered before clinical application of MSC-mediated cancer therapy.
The midline and intralaminar thalamic nuclei

GLOSSARY: CL = central lateral; CM = center médian; DBS = deep brain stimulation; GABA = γ-aminobutyric acid; GPe = globus pallidus, external segment; GPi = globus pallidus, internal segment; LDT = laterodorsal tegmental nucleus; N accumbens = nucleus accumbens; Pf = parafascicular; PPT = pedunculopontine tegmental nucleus; ReT = reticular thalamic nucleus; SNr = substantia nigra, pars reticulata; TC = thalamocortical.
The role of epithelial–mesenchymal transition drivers ZEB1 and ZEB2 in mediating docetaxel‐resistant prostate cancer

Docetaxel is the main treatment for advanced castration‐resistant prostate cancer; however, resistance eventually occurs. The development of intratumoral drug‐resistant subpopulations possessing a cancer stem cell (CSC) morphology is an emerging mechanism of docetaxel resistance, a process driven by epithelial–mesenchymal transition (EMT). This study characterised EMT in docetaxel‐resistant sublines through increased invasion, MMP‐1 production and ZEB1 and ZEB2 expression. We also present evidence for differential EMT across PC‐3 and DU145 in vitro resistance models as characterised by differential migration, cell colony scattering and susceptibility to the CSC inhibitor salinomycin. siRNA manipulation of ZEB1 and ZEB2 in PC‐3 and DU145 docetaxel‐resistant sublines identified ZEB1, through its transcriptional repression of E‐cadherin, to be a driver of both EMT and docetaxel resistance. The clinical relevance of ZEB1 was also determined through immunohistochemical tissue microarray assessment, revealing significantly increased ZEB1 expression in prostate tumours following docetaxel treatment. This study presents evidence for a role of ZEB1, through its transcriptional repression of E‐cadherin to be a driver of both EMT and docetaxel resistance in docetaxel‐resistant prostate cancer. In addition, this study highlights the heterogeneity of prostate cancer and in turn emphasises the complexity of the clinical management of docetaxel‐resistant prostate cancer.
A Basic Language Resource Kit Implementation for the IgboNLP Project

Igbo, an African language with around 32 million speakers worldwide, is one of the many languages having few or none of the language processing resources needed for advanced language technology applications. In this article, we describe the approach taken to creating an initial set of resources for Igbo, including an electronic text corpus, a part-of-speech (POS) tagset, and a POS-tagged subcorpus. We discuss the approach taken in gathering texts, the preprocessing of these texts, and the development of the POS tagged corpus. We also discuss some of the problems encountered during corpus and tagset development and the solutions arrived at for these problems.
Surgical Treatment of Graves' Disease: Comparison between Total Thyroidectomy and Subtotal Thyroidectomy

Purpose: Subtotal thyroidectomy has been the standard operation for Graves’ disease in achieving a favorable outcome in recovery of euthyroid state. However, the postoperative outcomes following subtotal thyroidectomy differ by surgeon and postoperative thyroid dysfunctions develop as time passes. Here, we have studied the validity of total thyroidectomy for Graves’ disease patients, with a comparison to subtotal thyroidectomy. Methods: A total of 299 patients with Graves’ disease underwent thyroid operation consecutively in Asan Medical Center, Seoul, Korea from December 1995 to December 2005. Among them, 241 cases had subtotal thyroidectomy and 43 had total thyroidectomy. The subtotal thyroidectomy cases were divided into 3 groups according to estimated remnant thyroid; ＜4 g, 4≤∼＜6 g and ≥6 g. Also, according to postoperative thyroid function, the patients were divided into euthyroid, hypothyroidism and hyperthyroidism groups. The postoperative changes of thyroid function, postoperative complications and hospital days were analyzed. Results: In subtotal thyroidectomy, postoperative thyroid function showed euthyroid in 25 (10.4%), hypothyroidism 206 (85.5%) and hyperthyroidism 10 (4.1%). However, total thyroidectomy showed no persistent hyperthyroidism or recurrence. The postoperative thyroid function state changed in 24 patients out of 148 who had more than 2 years postoperative follow-up. Hyper-functional changes developed with higher rates (Hypo-6 vs. hyper-18). The postoperative complication rate was higher in subtotal thyroidectomy including bleeding, hoarseness and hypocalcemia. Conclusion: In our study, the patients showing normal thyroid function after subtotal thyroidectomy were very limited and thyroid dysfunction developed continuously with time lapse, especially towards hyperthyroid state. Therefore, we suggest that total thyroidectomy should be considered as a treatment option in Graves’ disease. (J Korean Surg Soc 2009;77:82-87)