Miracle-dz/UniFAR-FTUs huggingface dataset:
Title: Tracking donor-reactive T cells: evidence for clonal deletion in tolerant kidney transplant patients

: T cell responses to allogeneic major histocompatibility (MHC) antigens present a formidable barrier to organ transplantation, necessitating long-term immunosuppression to minimize rejection. Chronic rejection and drug-induced morbidities are major limitations that could be overcome by allograft tolerance induction. Tolerance was first intentionally induced in humans via combined kidney and bone marrow transplantation (CKBMT), but the mechanisms of tolerance in these patients are incompletely understood. We now establish an assay to identify donor-reactive T cells and test the role of deletion in tolerance after CKBMT. Using high-throughput sequencing of the TCRB chain CDR3 region, we define a fingerprint of the donor-reactive T cell repertoire prior to transplantation and track those clones post-transplant. We observed post-transplant reductions in donor-reactive T cell clones in three tolerant CKBMT patients; such reductions were not observed in a fourth, non-tolerant, CKBMT patient or in two conventional kidney transplant recipients on standard immunosuppressive regimens. T cell repertoire turnover due to lymphocyte-depleting conditioning only partially accounted for the observed reductions in tolerant patients; in fact, conventional transplant recipients showed expansion of circulating donor-reactive clones, despite extensive repertoire turnover. Moreover, loss of donor-reactive T cell clones more closely associated with tolerance induction than in vitro functional assays. Our analysis supports clonal deletion as a mechanism of allograft tolerance in CKBMT patients. The results validate the significance of donor-reactive T cell clones identified pre-transplant by our method, supporting further exploration as a potential biomarker of transplant outcomes. T2 stim samples) and CKBMT Subjects 1 and 2, MLRs were set up using purified T-cells as responders. Previously frozen pre-transplant PBMCs were thawed, washed, and resuspended in MACS buffer. MACS beads (Pan T cell Isolation Kit II, Miltenyi Biotec catalog # 130-091-156) were used to generate “untouched” T cells. These T cells were resuspended in PBS at 1x10 6 cells/mL, labeled with CFSE at a concentration of 0.2uM-0.5uM (CellTrace CFSE Proliferation Kit, Molecular Probes TM (catalog # C34554), washed 3 times, and resuspended in MLR medium (AIM-V supplemented with 5% AB heat-inactivated human serum, 0.01M HEPES, and 50 uM 2-ME at a concentration of 2x10 6 cells/mL. For HC #2 and #3, CKBMT Subjects 4 and 5, the two conventional transplant recipients, and the anti-third party responses, whole PBMC were used as responders instead of purified T cells. PBMCs were labeled with CFSE as above and resuspended at 2x10 6 cells/mL. Preparation of violet dye-labeled stimulators: Cryopreserved donor (or healthy control) PBMCs were thawed, washed, resuspended in PBS, and labeled with BD Horizon TM Violet Proliferation Dye 450 (catalog # 562158). After labeling, cells were washed twice, resuspended in MLR medium at 2x10 6 cells/mL, and irradiated at 30-35 Gray.
ESTIMATION OF GENETIC PARAMETERS OF AUTOSOMAL AND SEX-LINKED PRE-WEANING TRAITS IN MAKUIE SHEEP USING MULTIVARIATE ANALYSIS pre-weaning

Estimation of genetic of autosomal and sex-linked traits in sheep using analysis. - Vol 51, No.2, 365-375. The objective of this study was to determine the genetic parameters of autosomal and sex-linked effects for birth weight (BW), weaning weight (WW), average daily gain from birth to weaning (ADG) and kleiber ratio (KR) of Makuie sheep. The data set used in this study was collected at Makuie sheep breeding station in West Azerbaijan province, Iran, between 1994 and 2011. The fixed effects included herd-year, sex (male or female), birth type (single or twin), and age of dam (five classes, 2-6 years old). The three multivariate linear animal models including direct (autosomal and sex-linked) and maternal effects were used to analyze data. The 2 nd model (including direct additive genetic effects of animal (autosomal and sex-linked) and permanent environmental effects), with the lowest AIC value was considered as the most appropriate model. Based on the most appropriate fitted model, direct autosomal and sex-linked heritabilities of BW, WW, ADG and KR were magnitude of sex-linked variances as a proportion of phenotypic variance obtained the best for BW, WW, ADG and KR, respectively. autosomal and sex-linked maternal permanent phenotypic maternal effects, and it could contribute to a more accurate estimation of the direct autosomal heritability. these results, rate Makuie moderate and high heritable traits, a genetic progress selection programs. Also, the obtained maternal permanent environmental effect for KR was 0.09 in this research which is in agreement with those reported by MOHAMMADI et al . (2015) in Lori sheep and GHAFOURI - KESBI , (2013) in Mehraban sheep. In this study, results show an increased trend in direct autosomal heritability estimates from birth to later ages. Similar results were reported by BAHREINI - BEHZADI et al . (2007); TOSH and KEMP , (1994) and GIZAW et al . (2007) in Kermani, Polled Dorset and Menz sheep, respectively.
function in programmed cell death

the data. contribution in required occur in independent of the of the Systematic genetic analyses with retrograde signaling mutants reveal that 3’-phosphoadenosine 5’-phosphate (PAP), a retrograde signal that modulates nuclear gene expression in response to stress, can cell and innate immunity via inhibition of the processing 5’-3’ exoribonucleases (XRNs). Our results provide evidence for the role of chloroplast-derived signal and RNA metabolism in the control of cell death and biotic stress response. both forward and reverse genetics on the mips1 mutant. An extragenic secondary mutation in divinyl protochlorophyllide 8-vinyl reductase involved in chlorophyll biosynthesis leads to chlorophyll deficiency that abolishes the mips1 cell death phenotype, as do changes in CO 2 availability. These findings provide evidence for a link between photosynthetic activity and PCD induction in mips1 . Additionally, we investigated the contribution of several retrograde signaling pathways to the control of PCD in mips1. This process was independent of GENOMES UNCOUPLED (GUN) and EX signaling pathways, but we found that SAL1-PAP_XRN retrograde signaling pathway inhibits cell death as well as basal defense reactions in Arabidopsis. Chloroplast-generated reactive oxygen species play a major role in localized cell death the non-host interaction Xanthomonas
Effects of aloe vera (Aloe barbadensis Miller) gel on growth performance and haemato-biochemical profiles in broiler chickens

The study was designed to assess the effects of aloe vera gel (AVG) on broiler growth performance and haemato-biochemical changes. “Lohman” day-old broiler chicks (n=48) were reared for 28 days. At day 13, chicks were randomly divided into four equal groups (12/group). Group A was non-treated control. Group B was supplemented with antibiotic (oxytetracycline hydrochloride) as a growth promoter in water. Group C and D were supplied AVG (1% and 2%) in drinking water. Antibiotic and AVG treated broilers had higher (P<0.05) live weight (1803.8 ± 63.6 gm and 1800.00 ± 64.2 gm) than control (1607.5 ± 41.7 gm). Total erythrocyte count (3.6 ± 0.1 x 106/uL), haemoglobin (9.9 ± 0.1 gm%) and packed cell volume (35.2 ± 0.4 %) were higher (P<0.05) in treated groups. It is suggested that the aloe vera gel supplementation (1-2%) may be used as an alternative to antibiotics for better growth performance in broilers without deleterious effects on haematobiochemical profiles. The Bangladesh Veterinarian (2019) 36(1 - 2): 25-32
The eﬀective Shafarevich conjecture for abelian varieties of GL 2 -type

In this article we establish the eﬀective Shafarevich conjecture for abelian varieties over Q of GL 2 -type. The proof combines Faltings’ method with Serre’s modularity conjecture, isogeny estimates and results from Arakelov theory. Our result opens the way for the eﬀective study of integral points on certain higher dimensional moduli schemes such as, for example, Hilbert modular varieties.
Modeling Cornelia de Lange Syndrome in vitro and in vivo reveals a role for cohesin complex 1 in neuronal survival and differentiation 2

29 Cornelia de Lange Syndrome (CdLS), which is reported to affect about 1 in 10,000 to 30,000 30 newborns, is a multisystem organ developmental disorder with relatively mild to severe effects. 31 Among others, intellectual disability represents an important feature of this condition. 32 Cornelia de Lange syndrome can result from mutations in at least five genes: NIPBL (nipped-B-like 33 protein) , SMC1A (structural maintenance of chromosomes 1A) , SMC3 (structural maintenance of 34 chromosomes 3) , RAD21 (RAD21 Cohesin Complex Component) , and HDAC8 (Histone deacetylase 35 8). It is believed that mutations in these genes cause CdLS by impairing the function of the cohesin 36 complex (to which all the aforementioned genes contribute to the structure or function), disrupting 37 gene regulation during critical stages of early development. Since result from studied the role of Hdac8 gene in mouse neural stem cells and in vertebrate ( D.rerio ) brain development by knock-down and chemical inhibition experiments. An underlying features of deficiency is an increased cell death in the developing tissues, either mouse NSCs 42 and in zebrafish
The Crystal Lattice: Phonons, Solitons, Dislocations

CLASSICAL DYNAMICS OF A CRYSTAL LATTICE. Vibrations of Monatomic Lattices. Models of Crystals of Various Dimensions. Vibrations of Polyatomic Lattices. Frequency Spectrum and Its Relation to the Green Function. Nonlinear Dynamics of One-Dimensional Crystals. QUANTUM MECHANICS OF CRYSTALS. Quantization of Crystal Vibrations. Interaction of Excitations in a Crystal. Quantum Crystals. CRYSTAL LATTICE DEFECTS. Point Defects. Linear Crystal Defects. Localization of Vibrations. Localization of Vibrations near Extended Defects. Elastic Field of Dislocations in a Crystal. Dislocation Dynamics. Subject Index.
The role of birth month in the burden of hospitalisations for acute lower respiratory infections due to respiratory syncytial virus in young children in Croatia

Background Birth month was an important risk factor for respiratory syncytial virus (RSV) hospitalisation in infants. However, little is known about the role of birth month in RSV hospitalisation in finer age bands during infancy, which is relevant to strategies for RSV passive immunisations for infants. We aimed to understand the role of birth month in the burden of RSV-associated acute lower respiratory infection (ALRI) hospitalisation in finer age bands of the first year of life. Methods In this retrospective study, we analysed the hospitalisation records during 2014–19 at the University Hospital of Split, Split-Dalmatia County, Croatia. We estimated all-cause and RSV associated ALRI hospitalisation rates among children under five years, with a focus on infants by finer age band and birth month. Results We included 1897 ALRI hospitalisations during the study period. Overall in children under five years, annual hospitalisation rate was 14.66/1000 (95% CI: 14.01–15.34) for all-cause ALRI, and was 7.56/1000 (95% CI: 6.83–8.34) for RSV-ALRI. RSV-ALRI hospitalisation rate was highest in infants aged 28 days–<3 months (61.15/1000, 95% CI: 52.91–70.31). Infants born in November, December and January (2–3 months before RSV peak) had the highest hospitalisation rates during infancy. Depending on the birth month of infants, the risk of RSV-ALRI hospitalisation peaked at different months of age; infants who were born in September had the highest RSV-ALRI hospitalisation rate at the age of 3–<6 months. Conclusions Our study underlines the importance of birth month in planning RSV immunisation strategies for infants, and provides useful baseline data for effectiveness analysis of novel RSV prophylactic products.
Characterizing Physiological Responses to Fear, Frustration, and Insight in Virtual Reality

Physiological sensing often complements studies of human behavior in virtual reality (VR) to detect users' affective and cognitive states. Some psychological states, such as fear and frustration, can be particularly hard to differentiate from a physiological perspective as they are close in the arousal and valence emotional space. Moreover, it is largely unclear how users' physiological reactions are expressed in response to transient psychological states such as fear, frustration, and insight—especially since these are rich indicators for characterizing users' responses to dynamic systems but are hard to capture in highly interactive settings. We conducted a study ($N=24$) to analyze participants' pulmonary, electrodermal, cardiac, and pupillary responses to moments of fear, frustration, and insight in immersive settings. Participants interacted in five VR environments, throughout which we measured their physiological reactions and analyzed the patterns we observed. We also measured subjective fear and frustration using questionnaires. We found differences between fear and frustration pupillary, respiratory, and electrodermal responses, as well as between the pupillary changes that followed fear in a horror game and those that followed fear in a vertigo experiment. We present the relationships between fear levels, frustration levels, and their physiological responses. To detect these affective events and states, we introduce user-independent binary classification models that achieved an average micro $F_{1}$ score of 71% for detecting fear in a horror game, 75% for fear of vertigo, 76% for frustration, and 75% for insight, showing the promise for detecting these states from passive and objective signals.
Robust Method for Screening Sleep Apnea With Single-Lead ECG Using Deep Residual Network: Evaluation With Open Database and Patch-Type Wearable Device Data

This paper proposes a robust method to screen patients with sleep apnea syndrome (SAS) using a single-lead electrocardiogram (ECG). This method consists of minute-by-minute abnormal breathing detection and apnea-hypopnea index (AHI) estimation. Heartbeat interval and ECG-derived respiration (EDR) are calculated using the single-lead ECG and used to train the models, including ResNet18, ResNet34, and ResNet50. The proposed method, using data from 1232 subjects, was developed with two open datasets and experimental data and evaluated using two additional open datasets and data acquired from an abdomen-attached wearable device (in total, data from 189 subjects). ResNet18 showed the best results, having an average Cohen's kappa coefficient of 0.57, in the abnormal breathing detection. Moreover, SAS patient classification, with 15 as the AHI threshold, yielded an average Cohen's kappa coefficient of 0.71. The results of patient classification were biased toward data from the wearable patch-type device, which may be influenced by different ECG waveforms. The proposed method is tuned with a sample of the data from the device, and the performance result of Cohen's kappa increased from 0.54 to 0.91 for SAS patient classification. Our method, proposed in this paper, achieved equivalent performance results with data recorded using an abdomen-attached wearable device and two open datasets used in previous studies, although the method had not used those data during model training. The proposed method could reduce the development costs of commercial software, as it was developed using open datasets, has robust performance throughout all datasets.
Copy number variation of EIF4A2 loci related to phenotypic traits in Chinese cattle

Abstract Background Generally, copy number variation (CNV) is a large‐scale structural variation between 50 bp and 1 kb of the genome. It can affect gene expression and is an important reason for genetic diversity and phenotypic trait diversity. Studies have shown that the eukaryotic translation initiation factor 4A2 (EIF4A2) gene plays an essential role in muscle development in both humans and pigs. However, the influence of bovine EIF4A2’s copy number change on phenotypic traits has not been reported. Objectives To detect the tissue expression profile of the EIF4A2 gene in adult cattle and individuals’ CNV type of variation. Then, we explored the correlation between EIF4A2‐CNV and growth traits in Chinese cattle breeds. Methods Real‐time fluorescent quantitative reverse transcription PCR (qRT‐qPCR) was used to determine the expression profile of the EIF4A2 gene. Real‐time fluorescent quantitative PCR (qPCR) was used to detect the CNV type of bovine populations. Then, SPSS 26.0 was used for association analysis. Results In this study, a total of 513 individuals in four cattle breeds (Qinchuan cattle [QC], Yunling cattle [YL], Pinan cattle [PN] and Jiaxian cattle [JX]) were detected for EIF4A2 gene's CNV. The results showed that EIF4A2‐CNV has an essential impact on hip width (HW) and rump length (RL) in QC, heart girth (HG), chest depth (CD) and RL in YL and HW in PN. However, it had no significant effect on JX. Conclusions The above results suggest that EIF4A2 gene's CNV can be used as a molecular marker for cattle breeding, which is helpful to accelerate the breeding of superior beef cattle breeds.
TapeTouch: A Handheld Shape-changing Device for Haptic Display of Soft Objects

Haptic feedback is widely used to enhance realism in virtual reality (VR). Shape and softness are two common factors perceived by the users in the haptic rendering of soft objects. To integrate these factors, we propose a new handheld shape-changing device, TapeTouch, to provide various shapes and softness in real time. TapeTouch is based on a controllable shape-changing tape, which is mainly composed of four motors and a section of brass tape. We design a structure of the components to fit a portable controller and allow to flexibly adjust the shape of the brass tape. After decoding desired shapes into the signals to control the motor, we automatically reproduce varying shapes and levels of softness to the finger or palm touching the shape-changing tape. We conducted two user studies to understand the capability of TapeTouch to render shape and softness, and the results showed that TapeTouch could provide a variety of distinguishable shapes as well as multiple levels of softness. Based on the results, we performed two VR experience studies to verify that the haptic feedback from TapeTouch enhances VR realism.
Numerical Experiments on the Stability of Spherical Stellar Systems

The concentric shell model is used to investigate numerically the stability of spherical steady-state stellar systems. Polytropic models with an isotropic velocity distribution are found to be stable almost down to the limiting index n=1/2. ‘Generalized polytropes’, with a distribution function depending on energy and angular momentum, show instability when n is low and the velocity distribution is radially elongated.
Angiographic Patency of Coronary Artery Bypass Conduits: An Updated Network Meta-Analysis of Randomized Trials

Introduction The second best conduit for coronary artery bypass grafting is uncertain. The objective of this study is to determine the second best conduit according to graft patency results from randomized controlled trials using a network meta-analysis. Methods A systematic literature search was conducted for randomized controlled trials comparing the angiographic patency rate of the no-touch saphenous vein (NT-SV), the radial artery (RA), the right internal thoracic artery (RITA), and the gastroepiploic artery (GEA) in reference to the conventionally harvested saphenous vein (CON-SV). The primary outcome was graft occlusion, and the secondary outcome was all-cause mortality. Results A total of 859 studies were retrieved, of which 18 were included. A total of 6,543 patients and 8,272 grafts were analyzed. The weighted mean angiographic follow-up time was 3.5 years. Compared with CON-SV, RA (incidence rate ratio [IRR] 0.56; 95% confidence interval [CI], 0.43-0.74) and NT-SV (IRR 0.56; 95% CI, 0.44-0.70) demonstrated lower graft occlusion. NT-SV and RA were ranked as the best conduits (rank score for NT-SV 0.88 vs. 0.87 for RA, 0.29 for GEA, 0.27 for CON-SV, and 0.20 for RITA). There was no significant difference in late mortality between different conduit types. Conclusion RA and NT-SV are associated with significantly lower graft occlusion rates and are comparably ranked as the best conduit for patency.
Epileptic Seizure Classification Using Battle Royale Search and Rescue Optimization-Based Deep LSTM

Epilepsy is a severe threat to society due to the treatment time, cost, and unpredictable nature of the disease, thereby imposing an urgent need for intelligent analysis. Electroencephalogram (EEG) is a commonly deployed test for detecting epilepsy that analyses the electrical activity of an individual's brain. This work proposes an optimized deep sequential model to improve the seizure classification performance based on a hybrid feature set derived from EEG signals. A novel hybridized Battle Royale Search and Rescue optimization (BRRO) algorithm is proposed for optimizing a deep learning (DL) model. Also, the proposed hybrid feature set utilizes empirical mode decomposition, variational mode decomposition, and empirical wavelet transform to capture the temporal property of the data set. The proposed method is validated using publicly available data sets. The results manifest that the proposed optimized algorithm provides better results than the other alternatives.
How spiritual leadership affects team safety performance: the role of team reflexivity and work interdependence

Objectives. Frequent occurrence of workplace accidents may be caused by a lack of attention by team members to safety behaviors on the spiritual level. It is very important to investigate the incentive mechanism of spirit factor on team safety performance. Methods. Based on social cognition theory and social interaction theory, this study analyzed matching data from 717 employees across 173 teams, and verified the mechanism underlying team-level spiritual leadership on team safety performance. Results. Spiritual leadership not only helped improved a team’s safety performance, but also affected it through team reflexivity. Meanwhile, work interdependence positively moderated the positive relationship between team reflexivity and team safety performance, as well as the mediating role of team reflexivity. Conclusions. The findings expanded the research scope of leadership style–safety performance at the team level, and provided guidelines for managers to promote safety and healthy development of a team in practice.
Cochlear implant outcomes in patients with Meniere’s disease: a large case series

Objective: To perform a matched cohort study to assess whether patients with Meniere's Disease (MD) require more intensive auditory rehabilitation following cochlear implantation (CI) and identify factors that may affect outcomes in patients with MD. Methods: A retrospective case review was performed. MD and control patients were matched for age, biological sex, implant manufacturer and electrode design. Outcomes measured were speech scores, number of visits to audiology department following switch-on, and post-operative active MD. Results: Forty consecutive implanted MD patients were identified between May 1993 and May 2019. Patients with active MD following CI required significantly more visits to the audiology department compared to controls (P < 0.01) and patients who had inactive MD post-operatively (P < 0.01). However, in MD patients, active MD was less likely following CI (P = 0.03). In patients who continued to experience active MD post-operatively, further medical and surgical ablative intervention was required to control ongoing Meniere's attacks. Conclusion: We present the largest case series of performance outcomes in CI patients with MD. Although speech outcomes in MD patients are comparable to controls, patients with active MD pre-operatively are more likely to experience variation in CI performance requiring a prolonged period of auditory rehabilitation compared to inactive preoperative MD.