Miracle-dz/UniFAR-FTUs huggingface dataset:
Transgenic mouse and cell culture models demonstrate a lack of mechanistic connection between endoplasmic reticulum stress and tau dysfunction

In vivo aggregation of tau protein is a hallmark of many neurodegenerative disorders, including Alzheimer's disease (AD). Recent evidence has also demonstrated activation of the unfolded protein response (UPR), a cellular response to endoplasmic reticulum (ER) stress, in AD, although the role of the UPR in disease pathogenesis is not known. Here, three model systems were used to determine whether a direct mechanistic link could be demonstrated between tau aggregation and the UPR. The first model system used was SH‐SY5Y cells, a neuronal cultured cell line that endogenously expresses tau. In this system, the UPR was activated using chemical stressors, tunicamycin and thapsigargin, but no changes in tau expression levels, solubility, or phosphorylation were observed. In the second model system, wild‐type 4R tau and P301L tau, a variant with increased aggregation propensity, were heterologously overexpressed in HEK 293 cells. This overexpression did not activate the UPR. The last model system examined here was the PS19 transgenic mouse model. Although PS19 mice, which express the P301S variant of tau, display severe neurodegeneration and formation of tau aggregates, brain tissue samples did not show any activation of the UPR. Taken together, the results from these three model systems suggest that a direct mechanistic link does not exist between tau aggregation and the UPR. © 2010 Wiley‐Liss, Inc.
IgE and risk of cancer in 37 747 individuals from the general population.

BACKGROUND Immunoglobulin E (IgE) is produced by plasma cells, often as part of an allergic immune response. It is currently unknown whether plasma IgE levels are associated with risk of cancer in individuals from the general population. We tested the hypothesis that high levels of plasma total IgE are associated with overall risk of cancer and with risk of specific cancers. MATERIALS AND METHODS Plasma total IgE was measured in 37 747 individuals from the general population, and the participants were followed prospectively for up to 30 years. All statistical tests were two-sided. RESULTS During a mean follow-up of 7 years, a first cancer was diagnosed in 3454 participants. The multivariable adjusted hazard ratio for a 10-fold higher level of IgE was 1.05 [95% confidence interval (CI) 1.00-1.11; P = 0.04] for any cancer, 0.44 (0.30-0.64; P = 0.00002) for chronic lymphocytic leukemia (CLL), 0.53 (0.33-0.84; P = 0.007) for multiple myeloma, 1.54 (1.04-2.29; P = 0.03) for other non-Hodgkin lymphoma, 1.38 (1.04-1.84; P = 0.03) for cancer of the oral cavity and pharynx, and 1.12 (1.00-1.25; P = 0.05) for lung cancer. The findings for CLL and multiple myeloma were generally robust; however, after correcting for 27 multiple comparisons only the finding for CLL remained significant. CONCLUSION High levels of plasma total IgE were associated with low risk of CLL and possibly of multiple myeloma, without convincing evidence for high risk of any cancer type.
Equimolar generation of the four possible arrangements of adjacent L components in herpes simplex virus type 1 replicative intermediates

Herpes simplex virus type 1 (HSV-1) replication generates high-molecular-weight intermediates containing branched DNA and concatemers carrying adjacent genomes with inverted L components. We have studied replicative intermediates generated by (i) wild-type HSV-1; (ii) 5dl1.2, an ICP27 null mutant which fails to synthesize normal amounts of DNA and late proteins; (iii) RBMu3, a mutant containing a deletion in the inverted repeats which fails to generate genomic isomers; and (iv) amplicon plasmids and vectors which contain no inverted sequences. Replication intermediates were analyzed by pulsed-field gel electrophoresis, after restriction enzyme digestion of infected-cell DNA, followed by blot hybridization. DNA fragments were statistically quantified after phosphorimaging. We observed that (i) the four possible configurations of L components of two adjacent genomes in the concatemers are present at equimolar amounts at any time during virus replication, (ii) ICP27 is not required for inversions or for branched DNA to occur, and (iii) replication intermediates of both RBMu3 mutant and amplicon plasmids or vectors do contain branched structures, although the concatemers they generate contain no inversions. These data indicate that inversions are generated by a mechanism intrinsically linked to virus DNA replication, most likely homologous recombination between inverted repeats. Branched structures are detected in all replicating molecules, including those that do not invert, suggesting that they are constitutively linked to virus DNA synthesis. Our results are consistent with the notion that the four HSV-1 genomic isomers are generated by alternative cleavage frames of replication concatemers containing equimolar amounts of L-component inversions.
Frame Stacking and Retaining for Recurrent Neural Network Acoustic Model

Frame stacking is broadly applied in end-to-end neural network training like connectionist temporal classification (CTC), and it leads to more accurate models and faster decoding. However, it is not well-suited to conventional neural network based on context-dependent state acoustic model, if the decoder is unchanged. In this paper, we propose a novel frame retaining method which is applied in decoding. The system which combined frame retaining with frame stacking could reduces the time consumption of both training and decoding. Long short-term memory (LSTM) recurrent neural networks (RNNs) using it achieve almost linear training speedup and reduces relative 41\% real time factor (RTF). At the same time, recognition performance is no degradation or improves sightly on Shenma voice search dataset in Mandarin.
Feasibility and Efficacy of the Nintendo Wii Gaming System to Improve Balance Performance Post-Stroke: Protocol of a Phase II Randomized Controlled Trial in an Inpatient Rehabilitation Setting.

OBJECTIVE Balance deficits following stroke are common and debilitating. Commercially available gaming systems, such as the Nintendo(®) (Kyoto, Japan) Wii™, have been widely adopted clinically; however, there is limited evidence supporting their feasibility and efficacy for improving balance performance following stroke. The aim of this trial is to investigate the clinical feasibility and efficacy of using the Nintendo Wii gaming system as an adjunct to standard care to improve balance performance following stroke in an inpatient rehabilitation setting. SUBJECTS AND METHODS Thirty participants undergoing inpatient stroke rehabilitation will be recruited into this Phase II, single-blind, randomized controlled trial. Participants will be allocated into a Balance or Upper Limb Group, and both groups will perform activities using the Nintendo Wii in addition to their standard care. Participants will attend three 45-minute sessions per week, for a minimum of 2 and a maximum of 4 weeks. RESULTS The main focus of the study is to investigate the feasibility of the intervention protocol. This will be evaluated through recruitment, retention, adherence, acceptability, and safety. The Step Test and Functional Reach Test will be the primary efficacy outcomes. Secondary outcomes will include force platform, mobility, and upper limb measures. Assessments will occur at baseline, 2 weeks, and 4 weeks after study entry. DISCUSSION To the authors' knowledge, this will be the largest randomized clinical trial to investigate the feasibility and efficacy of the Nintendo Wii gaming system for improving balance performance in a stroke population. The results will inform the design of a Phase III multicenter trial.
Genomic organization, chromosomal localization, and developmentally regulated expression of the glycosyl-phosphatidylinositol-specific phospholipase C of Trypanosoma brucei

The surface of the bloodstream form of the African trypanosome, Trypansoma brucei, is covered with about 10(7) molecules of the variant surface glycoprotein (VSG), a protein tethered to the plasma membrane by a glycosyl-phosphatidylinositol (GPI) membrane anchor. This anchor is cleavable by an endogenous GPI-specific phospholipase C (GPI-PLC). GPI-PLC activity is down regulated when trypanosomes differentiate from the bloodstream form to the procyclic form found in the tsetse fly vector. We have mapped the GPI-PLC locus in the trypanosome genome and have examined the mechanism for this developmental regulation in T. brucei. Southern blot analysis indicates a single-copy gene for GPI-PLC, with two allelic variants distinguishable by two NcoI restriction fragment length polymorphisms. The gene was localized solely to a chromosome in the two-megabase compression region by contour-clamped homogeneous electric field gel electrophoresis. No rearrangement of the GPI-PLC gene occurs during differentiation to procyclic forms, which could potentially silence GPI-PLC gene expression. Enzymological studies give no indication of a diffusible inhibitor of GPI-PLC activity in procyclic forms, and Western immunoblot analysis reveals no detectable GPI-PLC polypeptide in these forms. Therefore, it is highly unlikely that the absence of GPI-PLC activity in procyclic forms is due to posttranslational control. Northern (RNA) blot analysis reveals barely detectable levels of GPI-PLC mRNA in procyclic forms; therefore, regulation of GPI-PLC activity in these forms correlates with the steady-state mRNA level.
Analysis of Human Biologics With a Mouse Skin Transplant Model in Humanized Mice

Preclinical testing of human therapeutic monoclonal antibodies has been limited in murine models due to species differences in pharmacokinetics and biologic responses. To overcome these constraints we developed a murine skin transplant model in humanized mice and used it to test human monoclonal antibody therapy. Neonatal NOD/SCID/IL2Rγcnull mice (NSG) were reconstituted with human CD34+ hematopoietic stem cells (hNSG). When adult, these mice rejected MHC mismatched murine C57BL/6J skin grafts. Rejection required adequate reconstitution with human cells. There was diffuse infiltration of the epidermis and dermis with hCD8 and hCD4 cells in rejected grafts by immunohistochemistry. Studies with B6/MHC class I and II knockout mice donors indicated that neither is required for rejection. Graft rejection was associated with the development of effector and central memory T cells and an increase in serum immunoglobulins. We also tested the effects of teplizumab (anti‐CD3 mAb) and found it could delay skin graft rejection, whereas ipilimumab (anti‐CTLA‐4 [cytotoxic T‐lymphocyte antigen‐4] mAb) treatment accelerated rejection. These findings demonstrate that hNSG mice reliably and predictably reject a xenogenic mouse skin graft by a human T cell mediated mechanism. The model can be utilized to investigate the ability of human immunotherapies to enhance or suppress functional human immune responses.
4D Biofabrication Using Shape‐Morphing Hydrogels

Despite the tremendous potential of bioprinting techniques toward the fabrication of highly complex biological structures and the flourishing progress in 3D bioprinting, the most critical challenge of the current approaches is the printing of hollow tubular structures. In this work, an advanced 4D biofabrication approach, based on printing of shape‐morphing biopolymer hydrogels, is developed for the fabrication of hollow self‐folding tubes with unprecedented control over their diameters and architectures at high resolution. The versatility of the approach is demonstrated by employing two different biopolymers (alginate and hyaluronic acid) and mouse bone marrow stromal cells. Harnessing the printing and postprinting parameters allows attaining average internal tube diameters as low as 20 µm, which is not yet achievable by other existing bioprinting/biofabrication approaches and is comparable to the diameters of the smallest blood vessels. The proposed 4D biofabrication process does not pose any negative effect on the viability of the printed cells, and the self‐folded hydrogel‐based tubes support cell survival for at least 7 d without any decrease in cell viability. Consequently, the presented 4D biofabrication strategy allows the production of dynamically reconfigurable architectures with tunable functionality and responsiveness, governed by the selection of suitable materials and cells.
Nonparametric Splitting Algorithm for Detecting Structural Changes in Predictive Relationships

The problem of detecting structural changes in a regression study has become crucially important in a wide variety of fields, since data generating processes in a real world are usually unstable. Taking into account the fact that relationships within observed data are often in a continuous flux, it can be challenging to make any distributional assumptions. In the current paper, we propose a new nonparametric technique which allows estimation of an unknown number of structural change points in multivariate data having univariate response. The Nonparametric Splitting algorithm is a heuristic smart search for relationship changes based on a consequential division of the data into smaller parts. The approach utilizes a nonparametric change point test to find narrow regions of change locations. Our preliminary experiments are promising and suggest potential for the high efficiency and prediction accuracy of the introduced method.
Slipknotting upon native-like loop formation in a trefoil knot protein

Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate.
Long-term follow-up of patients with meningiomas involving the cavernous sinus: recurrence, progression, and quality of life.

OBJECTIVE In this report, we evaluate the recurrence- and progression-free survival of patients with meningiomas involving the cavernous sinus. METHODS The rates of tumor recurrence and progression in 119 patients with meningiomas involving the cavernous sinus treated between 1983 and 1993 were analyzed. RESULTS The mean follow-up period was 33.8 months. There were seven recurrences of completely resected tumors (7 of 73, 10%) and seven progressions of incompletely resected tumors (7 of 46 15%). Life table analysis of recurrence- and progression-free survival was performed. The recurrence-free survival rate was 94% at 3 years and 81% at 5 years. In contrast, the progression-free survival rate was 87% at 3 years and 62% at 5 years (P = 0.0456). There were two patterns of recurrence or progression. The first group of tumors had an aggressive biological behavior with growth at multiple areas of resection; the second group showed growth at or near the margins of resection. Functional status continued to improve slowly during the follow-up period; however, there was no statistically significant difference between the Karnofsky scores obtained 3 to 12 months postoperatively and the follow-up Karnofsky scores (obtained > 1 yr postoperatively). CONCLUSION Surgery for meningiomas involving the cavernous sinus seems to provide excellent tumor control. Our experience suggests that for the majority of these tumors, complete tumor resection can be performed with acceptable risks of morbidity and mortality and seems to increase the duration of recurrence-free survival. The long-term quality of life of surviving patients is satisfactory, with the great majority of the patients being independent.
Chloroplast microsatellite markers for Pseudotaxus chienii developed from the whole chloroplast genome of Taxus chinensis var. mairei (Taxaceae)1

Premise of the study: Pseudotaxus chienii (Taxaceae) is an old rare species endemic to China that has adapted well to ecological heterogeneity with high genetic diversity in its nuclear genome. However, the genetic variation in its chloroplast genome is unknown. Methods and Results: Eighteen chloroplast microsatellite markers (cpSSRs) were developed from the whole chloroplast genome of Taxus chinensis var. mairei and successfully amplified in four P. chienii populations and one T. chinensis var. mairei population. Of these loci, 10 were polymorphic in P. chienii, whereas six were polymorphic in T. chinensis var. mairei. The unbiased haploid diversity per locus ranged from 0.000 to 0.641 and 0.000 to 0.545 for P. chienii and T. chinensis var. mairei, respectively. Conclusions: The 18 cpSSRs will be used to further investigate the chloroplast genetic structure and adaptive evolution in P. chienii populations.
An Investigation of Symptom-Specific Muscle Hyperreactivity in Upper Extremity Cumulative Trauma Disorder

ObjectiveThe study examined symptom-specific muscle hyperreactivity in patients with chronic pain with upper limb cumulative trauma disorder (CTD). DesignFour tasks were presented in counterbalanced order and included neutral, general stressor, personal stressor, and pain stressor tasks. Ratings of stressfulness and recordings of skin conductance level confirmed the effectiveness of the experimental manipulations in inducing stress experiences for all subject groups. SettingThe study was conducted in a university research center. PatientsThirty patients with CTD were matched as closely as possible for age and gender to control groups of chronic low back pain, arthritis, and pain-free subjects. Outcome MeasuresSurface electromyograph recordings were taken from the frontalis, forearm flexors, trapezius, and lower back during baseline and tasks. ResultsThe study found no evidence of greater muscle tension increases or extended duration of return to baseline for the CTD or low back pain patients at any of the muscle sites for any of the tasks in comparison to control groups. ConclusionsThe results indicate that symptom-specific psychophysiological responses may be limited to certain subgroups rather than being characteristic of chronic musculoskeletal pain patients in general.
On spectral efficiency maximization in a partial joint processing system using a multi-start particle swarm optimization algorithm

Downlink joint processing (JP) between base stations eliminates the inter-cell interference in a cellular system with a frequency reuse factor of one and improves the spectral efficiency of cell-edge users. JP has a huge impact on both feedback and backhaul load, and thus partial JP was presented to tackle with signaling demand. However, achieving equivalent backhaul reduction based on limited feedback channel state information is challenging when linear techniques, such as zero-forcing beamforming (BF) are used, which led to the use of stochastic algorithms instead. Therefore stochastic multi-start particle swarm optimization algorithm (MSPSOA) is proposed in this paper to achieve backhaul reduction and address the issue of lack of diversity, which is related to the basic particle swarm optimization algorithm (BPSOA). The lack of diversity has been solved in this work by replacing the inactive particles adaptively based on a predefined constant which represents the difference between local best and global best optimization criterion. The performance of the proposed MSPSOA and BPSOA BF is evaluated with respect to full and partial JP using different metrics such as sum-rate, actual interference and convergence using a multipath realistic environment WINNER II channel model. The proposed MSPSOA outperforms BPSOA in terms of average sum-rate by 15.3%, while the actual interference decreased by 14.6% in some conducted scenarios.
Refining criteria for diagnosis of cutaneous infections caused by herpes viruses through correlation of morphology with molecular pathology.

BACKGROUND Infections of the skin by herpes viruses do not always present themselves in typical fashion. Early diagnosis, however, is crucial for appropriate treatment. Polymerase chain reaction (PCR) allows diagnosis and differential diagnosis of herpes virus infections, but the method is not yet available in large parts of the world, where diagnosis is made based on morphology alone. AIM To refine criteria for the diagnosis of herpes virus infections of the skin by way of correlation of clinical and histopathologic findings with results of PCR studies. METHODS We studied 75 clinically diagnosed patients of "zoster," "varicella," and "herpes simplex", to correlate clinical and histopathological findings with results of PCR studies on paraffin embedded biopsy specimens. RESULTS Clinical suspicion of infection by herpes viruses was confirmed by histopathology in 37% of the cases and by PCR studies in 65% of the cases. Zoster was frequently misdiagnosed as infection with herpes simplex viruses (30%). When diagnostic signs of herpes virus infection were encountered histopathologically, PCR confirmed the diagnosis in 94%. By way of correlation with results of PCR studies, initial lesions of herpes virus infections could be identified to have a distinctive histopathological pattern. Herpetic folliculitis appeared to be a rather common finding in zoster, it occurring in 28% of the cases. CONCLUSION We conclude that correlation of clinical and histopathological features with results of PCR studies on one and the same paraffin embedded specimen permits identification of characteristic morphologic patterns and helps to refine criteria for diagnosis both clinically and histopathologically.