Miracle-dz/UniFAR-FTUs huggingface dataset:
Induction and Exhaustion of Lymphocytic Choriomeningitis Virus–specific Cytotoxic T Lymphocytes Visualized Using Soluble Tetrameric Major Histocompatibility Complex Class I–Peptide Complexes

This study describes the construction of soluble major histocompatibility complexes consisting of the mouse class I molecule, H-2Db, chemically biotinylated β2 microglobulin and a peptide epitope derived from the glycoprotein (GP; amino acids 33–41) of lymphocytic choriomeningitis virus (LCMV). Tetrameric class I complexes, which were produced by mixing the class I complexes with phycoerythrin-labeled neutravidin, permitted direct analysis of virus-specific cytotoxic T lymphocytes (CTLs) by flow cytometry. This technique was validated by (a) staining CD8+ cells in the spleens of transgenic mice that express a T cell receptor (TCR) specific for H-2Db in association with peptide GP33–41, and (b) by staining virus-specific CTLs in the cerebrospinal fluid of C57BL/6 (B6) mice that had been infected intracranially with LCMV-DOCILE. Staining of spleen cells isolated from B6 mice revealed that up to 40% of CD8+ T cells were GP33 tetramer+ during the initial phase of LCMV infection. In contrast, GP33 tetramers did not stain CD8+ T cells isolated from the spleens of B6 mice that had been infected 2 mo previously with LCMV above the background levels found in naive mice. The fate of virus-specific CTLs was analyzed during the acute phase of infection in mice challenged both intracranially and intravenously with a high or low dose of LCMV-DOCILE. The results of the study show that the outcome of infection by LCMV is determined by antigen load alone. Furthermore, the data indicate that deletion of virus-specific CTLs in the presence of excessive antigen is preceded by TCR downregulation and is dependent upon perforin.
An optimized structure on FPGA of key point description in SIFT algorithm

SIFT algorithm is one of the most significant and effective algorithms to describe the features of image in the field of image matching. To implement SIFT algorithm to hardware environment is apparently considerable and difficult. In this paper, we mainly discuss the realization of Key Point Description in SIFT algorithm, along with Matching process. In Key Point Description, we have proposed a new method of generating histograms, to avoid the rotation of adjacent regions and insure the rotational invariance. In Matching, we replace conventional Euclidean distance with Hamming distance. The results of the experiments fully prove that the structure we propose is real-time, accurate, and efficient. Future work is still needed to improve its performance in harsher conditions.
Effect of Metformin on Vascular Function in Children With Type 1 Diabetes: A 12-Month Randomized Controlled Trial

Context Children with type 1 diabetes have vascular dysfunction preceding atherosclerosis. Early interventions are needed to reduce cardiovascular disease. Objective To evaluate the effect of metformin on vascular function in children with type 1 diabetes. Design Twelve-month double-blind, randomized, placebo-controlled trial. Setting Tertiary pediatric diabetes clinic. Participants Ninety children (8 to 18 years of age), >50th percentile body mass index (BMI), with type 1 diabetes. Intervention Metformin (up to 1 g twice a day) or placebo. Main Outcome Measure Vascular function measured by brachial artery ultrasound [flow-mediated dilatation/glyceryl trinitrate-mediated dilatation (GTN)]. Results Ninety participants were enrolled [41 boys, 13.6 (2.5) years of age, 45 per group], 10 discontinued intervention, and 1 was lost to follow-up. On metformin, GTN improved, independent of glycosylated hemoglobin (HbA1c), by 3.3 percentage units [95% confidence interval (CI) 0.3, 6.3, P = 0.03] and insulin dose reduced by 0.2 U/kg/d (95% CI 0.1, 0.3, P = 0.001) during 12 months, with effects from 3 months. Metformin had a beneficial effect on HbA1c at 3 months (P = 0.001) and difference in adjusted HbA1c between groups during 12 months was 1.0%; 95% CI 0.4, 1.5 (10.9 mmol/mol; 95% CI 4.4, 16.4), P = 0.001. There were no effects on carotid/aortic intima media thickness, BMI, lipids, blood pressure, or other cardiovascular risk factors. Median (95% CI) adherence, evaluated by electronic monitoring, was 75.5% (65.7, 81.5), without group differences. More gastrointestinal side effects were reported on metformin (incidence rate ratio 1.65, 95% CI 1.08, 2.52, P = 0.02), with no difference in hypoglycemia or diabetic ketoacidosis. Conclusions Metformin improved vascular smooth muscle function and HbA1c, and lowered insulin dose in type 1 diabetes children. These benefits and good safety profile warrant further consideration of its use.
“Positive” Results Increase Down the Hierarchy of the Sciences

The hypothesis of a Hierarchy of the Sciences with physical sciences at the top, social sciences at the bottom, and biological sciences in-between is nearly 200 years old. This order is intuitive and reflected in many features of academic life, but whether it reflects the “hardness” of scientific research—i.e., the extent to which research questions and results are determined by data and theories as opposed to non-cognitive factors—is controversial. This study analysed 2434 papers published in all disciplines and that declared to have tested a hypothesis. It was determined how many papers reported a “positive” (full or partial) or “negative” support for the tested hypothesis. If the hierarchy hypothesis is correct, then researchers in “softer” sciences should have fewer constraints to their conscious and unconscious biases, and therefore report more positive outcomes. Results confirmed the predictions at all levels considered: discipline, domain and methodology broadly defined. Controlling for observed differences between pure and applied disciplines, and between papers testing one or several hypotheses, the odds of reporting a positive result were around 5 times higher among papers in the disciplines of Psychology and Psychiatry and Economics and Business compared to Space Science, 2.3 times higher in the domain of social sciences compared to the physical sciences, and 3.4 times higher in studies applying behavioural and social methodologies on people compared to physical and chemical studies on non-biological material. In all comparisons, biological studies had intermediate values. These results suggest that the nature of hypotheses tested and the logical and methodological rigour employed to test them vary systematically across disciplines and fields, depending on the complexity of the subject matter and possibly other factors (e.g., a field's level of historical and/or intellectual development). On the other hand, these results support the scientific status of the social sciences against claims that they are completely subjective, by showing that, when they adopt a scientific approach to discovery, they differ from the natural sciences only by a matter of degree.
GWAlpha: genome‐wide estimation of additive effects (alpha) based on trait quantile distribution from pool‐sequencing experiments

Motivation: Sequencing pools of individuals (Pool‐Seq) is a cost‐effective way to gain insight into the genetics of complex traits, but as yet no parametric method has been developed to both test for genetic effects and estimate their magnitude. Here, we propose GWAlpha, a flexible method to obtain parametric estimates of genetic effects genome‐wide from Pool‐Seq experiments. Results: We showed that GWAlpha powerfully replicates the results of Genome‐Wide Association Studies (GWAS) from model organisms. We perform simulation studies that illustrate the effect on power of sample size and number of pools and test the method on different experimental data. Availability and Implementation: GWAlpha is implemented in python, designed to run on Linux operating system and tested on Mac OS. It is freely available at https://github.com/aflevel/GWAlpha. Contact: afournier@unimelb.edu. au Supplementary information: Supplementary data are available at Bioinformatics online.
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning

Medicinal chemistry patents contain rich information about chemical compounds. Although much effort has been devoted to extracting chemical entities from scientific literature, limited numbers of patent mining systems are publically available, probably due to the lack of large manually annotated corpora. To accelerate the development of information extraction systems for medicinal chemistry patents, the 2015 BioCreative V challenge organized a track on Chemical and Drug Named Entity Recognition from patent text (CHEMDNER patents). This track included three individual subtasks: (i) Chemical Entity Mention Recognition in Patents (CEMP), (ii) Chemical Passage Detection (CPD) and (iii) Gene and Protein Related Object task (GPRO). We participated in the two subtasks of CEMP and CPD using machine learning-based systems. Our machine learning-based systems employed the algorithms of conditional random fields (CRF) and structured support vector machines (SSVMs), respectively. To improve the performance of the NER systems, two strategies were proposed for feature engineering: (i) domain knowledge features of dictionaries, chemical structural patterns and semantic type information present in the context of the candidate chemical and (ii) unsupervised feature learning algorithms to generate word representation features by Brown clustering and a novel binarized Word embedding to enhance the generalizability of the system. Further, the system output for the CPD task was yielded based on the patent titles and abstracts with chemicals recognized in the CEMP task. The effects of the proposed feature strategies on both the machine learning-based systems were investigated. Our best system achieved the second best performance among 21 participating teams in CEMP with a precision of 87.18%, a recall of 90.78% and a F-measure of 88.94% and was the top performing system among nine participating teams in CPD with a sensitivity of 98.60%, a specificity of 87.21%, an accuracy of 94.75%, a Matthew’s correlation coefficient (MCC) of 88.24%, a precision at full recall (P_full_R) of 66.57% and an area under the precision-recall curve (AUC_PR) of 0.9347. The SSVM-based CEMP systems outperformed the CRF-based CEMP systems when using the same features. Features generated from both the domain knowledge and unsupervised learning algorithms significantly improved the chemical NER task on patents. Database URL: http:// database. oxfordjournals. org/ content/ 2016/ baw049
Industrial Approach to Design a 2-kVa Inverter for Google Little Box Challenge

Uninterruptible power system, photovoltaics inverters, home appliances, motor drives, and automotive systems require highly efficient, reliable, and compact single-phase inverters. This paper presents different industrial design approach and experimental performance of high power density (100 W/in3) single-phase inverter with power output of 2 kVA that was presented for Google Little Box challenge. Multiple technical challenges were addressed, different methodologies described to achieve high power density and high efficiency reliable design. High power density was achieved by using the combination of optimized forced air cooled heatsinks, fully digital control, optimized component packaging, and by the introduction of a series active filter that enabled to reduce the size of dc bus capacitors. Low-loss high flux density magnetic materials such as Amoflux powder iron for power inductors and nanocrystalline magnetic materials for electromagnetic interference filter were also used. To minimize inverter switching losses, SiC devices operating at low switching frequency were adopted. Also, an innovative ground current control strategy is devised to minimize the ground leakage currents.
The ADAPTOR PROTEIN-3 Complex Mediates Pollen Tube Growth by Coordinating Vacuolar Targeting and Organization1[OPEN]

The dynamic organization of vacuoles and the association of tonoplast cargo protein PAT10 are impaired and lead to reduced pollen tube growth in adaptor protein-3 mutants. Pollen tube growth is an essential step for successful plant reproduction. Vacuolar trafficking and dynamic organization are important for pollen tube growth; however, the key proteins involved in these processes are not well understood. Here, we report that the ADAPTOR PROTEIN-3 (AP-3) complex and its tonoplast cargo PROTEIN S-ACYL TRANSFERASE10 (PAT10) are critical for pollen tube growth in Arabidopsis (Arabidopsis thaliana). AP-3 is a heterotetrameric protein complex consisting of four subunits, δ, β, µ, and σ. AP-3 regulates tonoplast targeting of several cargoes, such as PAT10. We show that functional loss of any of the four AP-3 subunits reduces plant fertility. In ap-3 mutants, pollen development was normal but pollen tube growth was compromised, leading to reduced male transmission. Functional loss of PAT10 caused a similar reduction in pollen tube growth, suggesting that the tonoplast association of PAT10 mediated by AP-3 is crucial for this process. Indeed, the Ca2+ gradient during pollen tube growth was reduced significantly due to AP-3 loss of function, consistent with the abnormal targeting of CALCINUERIN B-LIKE2 (CBL2) and CBL3, whose tonoplast association depends on PAT10. Furthermore, we show that the pollen tubes of ap-3 mutants have vacuoles with simplified tubules and bulbous structures, indicating that AP-3 affects vacuolar organization. Our results demonstrate a role for AP-3 in plant reproduction and provide insights into the role of vacuoles in polarized cell growth.
Oncology Nursing Perceptions of Patient Electronic Portal Use: A Qualitative Analysis

Purpose/Objectives: To identify nursing staff reactions to and perceptions of electronic portal use in a cancer setting. Research Approach: Qualitative. Setting: Outpatient clinic at the Harold C. Simmons Comprehensive Cancer Center of the University of Texas Southwestern Medical Center in Dallas. Participants: 13 nurses with a range of credentials and experience, representing infusion, medical oncology, and bone marrow transplantation clinics. Methodologic Approach: Two focus groups were conducted. Theoretical thematic content analysis of data was performed. Findings: Key themes that emerged for consideration of electronic portals included work volume and flow, patient expectations and safety, variation in use of communication technologies, and education and management. Interpretation: The current study provides insight into the implications of electronic portals by identifying nursing staff reactions to this technology. These reactions are predominantly related to the impact on clinical workload and patient safety and expectations. Implications for Nursing: As clinical cancer facilities incorporate electronic portal technology into their operations, attention to the impact on staff workload, division of labor, patient safety, and patient expectations should be considered.
Conflict monitoring and adaptation as reflected by N2 amplitude in obsessive–compulsive disorder

Background Feelings of doubt and perseverative behaviours are key symptoms of obsessive–compulsive disorder (OCD) and have been linked to hyperactive error and conflict signals in the brain. While enhanced neural correlates of error monitoring have been robustly shown, far less is known about conflict processing and adaptation in OCD. Method We examined event-related potentials during conflict processing in 70 patients with OCD and 70 matched healthy comparison participants, focusing on the stimulus-locked N2 elicited in a flanker task. Conflict adaptation was evaluated by analysing sequential adjustments in N2 and behaviour, i.e. current conflict effects as a function of preceding conflict. Results Patients with OCD showed enhanced N2 amplitudes compared with healthy controls. Further, patients showed stronger conflict adaptation effects on reaction times and N2 amplitude. Thus, the effect of previous compatibility was larger in patients than in healthy participants as indicated by greater N2 adjustments in change trials (i.e. iC, cI). As a result of stronger conflict adaptation in patients, N2 amplitudes were comparable between groups in incompatible trials following incompatible trials. Conclusions Larger N2 amplitudes and greater conflict adaptation in OCD point to enhanced conflict monitoring leading to increased recruitment of cognitive control in patients. This was most pronounced in change trials and was associated with stronger conflict adjustment in N2 and behaviour. Thus, hyperactive conflict monitoring in OCD may be beneficial in situations that require a high amount of control to resolve conflict, but may also reflect an effortful process that is linked to distress and symptoms of OCD.
Does Local Ibandronate and/or Pamidronate Delivery Enhance Osseointegration? A Systematic Review

PURPOSE To our knowledge from indexed literature, the present study is the first one to systematically review the influence of local delivery of pamidronate (PAM) and/or ibandronate (IBA) on osseointegration enhancement. The aim of the present systematic review was to assess the efficacy of IBA and/or PAM local delivery (topically or coating on implants surfaces) in promoting osseointegration. MATERIALS AND METHODS To address the focused question, "Does local IBA and/or PAM delivery enhances osseointegration? ," indexed databases were searched without time or language restrictions up to and including May 2016 using various combinations of the following keywords: "pamidronate," "ibandronate," "bisphosphonates," "osseointegration," and "topical administration. " Letters to the Editor, historic reviews, commentaries, case series, and case reports were excluded. RESULTS Fifteen studies were included. Fourteen studies were performed in animals and 2 were clinical trials. One study reported an experimental model and a clinical trial in the same publication. Results from 12 experimental studies and 2 clinical studies reported improved biomechanical properties and/or osseointegration around implants with PAM and/or IBA. Two experimental studies showed that PAM and/or IBA did not improve osseointegration. CONCLUSIONS On experimental grounds, local IBA and/or PAM delivery seems to enhance osseointegration; however, from a clinical perspective, further randomized control trials are needed to assess the effectiveness of IBA and PAM in promoting osseointegration around dental implants.
4D bioprinting: the next-generation technology for biofabrication enabled by stimuli-responsive materials

Four-dimensional (4D) bioprinting, encompassing a wide range of disciplines including bioengineering, materials science, chemistry, and computer sciences, is emerging as the next-generation biofabrication technology. By utilizing stimuli-responsive materials and advanced three-dimensional (3D) bioprinting strategies, 4D bioprinting aims to create dynamic 3D patterned biological structures that can transform their shapes or behavior under various stimuli. In this review, we highlight the potential use of various stimuli-responsive materials for 4D printing and their extension into biofabrication. We first discuss the state of the art and limitations associated with current 3D printing modalities and their transition into the inclusion of the additional time dimension. We then suggest the potential use of different stimuli-responsive biomaterials as the bioink that may achieve 4D bioprinting where transformation of fabricated biological constructs can be realized. We finally conclude with future perspectives.
Accuracy of digital implant impressions with intraoral scanners. A systematic review.

AIM The use of intraoral scanners (IOS) for making digital implant impressions is increasing. However, there is a lack of evidence on the accuracy of IOS compared with conventional techniques. Therefore, the aim of this systematic review was to collect evidence on the accuracy of digital implant impression techniques, as well as to identify the main factors influencing the accuracy outcomes. MATERIALS AND METHODS Two reviewers searched electronic databases in November, 2016. Controlled vocabulary, free-text terms, and defined inclusion and exclusion criteria were used. Publications in English language evaluating the accuracy outcomes of digital implant impressions were identified. Pooled data were analysed qualitatively and pertinent data extracted. RESULTS In total, 16 studies fulfilled the inclusion criteria: one in vivo and 15 in vitro studies. The clinical study concluded that angular and distance errors were too large to be acceptable clinically. Less accurate findings were reported by several in vitro studies as well. However, all in vitro studies investigating the accuracy of newer generation IOS indicated equal or even better results compared with the conventional techniques. Data related to the influence of distance and angulation between implants, depth of placement, type of scanner, scanning strategy, characteristics of scanbody and reference scanner, operator experience, etc were analysed and summarised. Linear deviations (means) of IOS used in in vitro studies ranged from 6 to 337 µm. Recent studies indicated small angle deviations (0.07-0.3°) with digital impressions. Some studies reported that digital implant impression accuracy was influenced by implant angulation, distance between the implants, implant placement depth and operator experience. CONCLUSIONS According to the results of this systematic review and based on mainly in vitro studies, digital implant impressions offer a valid alternative to conventional impressions for single- and multi-unit implant-supported restorations. Further in vivo studies are needed to substantiate the use of currently available IOS, identify factors potentially affecting accuracy and define clinical indications for specific type of IOS. Data on Data on accuracy OF digital records, as well as accuracy of printed or milled models for implant-supported restorations, are of high relevance and are still lacking. Conflict-of-interest and funding statement: The authors state there is no conflict of interest.
Coulomb Shapes: Using Electrostatic Forces for Deformation-invariant Shape Representation

Canonical shape analysis is a popular method in deformable shape matching, trying to bring the shape into a canonical form that undoes its non-rigid deformations, thus reducing the problem of non-rigid matching into a rigid one. The canonization can be performed by measuring geodesic distances between all pairs of points on the shape and embedding them into a Euclidean space by means of multidimensional scaling (MDS), which reduces the intrinsic isometries of the shape into the extrinsic (Euclidean) isometries of the embedding space. A notable drawback of MDS-based canonical forms is their sensitivity to topological noise: different shape connectivity can affect dramatically the geodesic distances, resulting in a global distortion of the canonical form. In this paper, we propose a different shape canonization approach based on a physical model of electrostatic repulsion. We minimize the Coulomb energy subject to the local distance constraints between adjacent shape vertices. Our model naturally handles topological noise, allowing to 'tear' the shape at points of strong repulsion. Furthermore, the problem is computationally efficient, as it lends itself to fast multipole methods. We show experimental results in which our method compares favorably to MDS-based canonical forms.