Miracle-dz/UniFAR-FTUs huggingface dataset:
Demyelinating Disease Regulatory T Cells During Autoimmune Modified Spreading Cascade with Genetically Pre-Emptive Targeting of the Epitope

4 Epitope spreading or endogenous self-priming has been implicated in mediating the progression of autoimmune disease. In the present study we created an immune-deviated, epitope spreading response in SWXJ mice after the onset of experimental autoimmune encephalomyelitis, a prototypic autoimmune animal model widely used in multiple sclerosis research. We established an immunoregulatory spreading repertoire by transferring T cells genetically modiﬁed to produce high levels of IL-10 in response to a dominant epitope spreading determinant. Installation of a Th2/Tr1-like spreading repertoire resulted in a marked and prolonged inhibition of disease progression and demyelination characterized by 1) bystander inhibition of the recall response to the priming immunogen, and 2) a Th1 3 Tr1 immune-deviated spreading response involving a shift in the source of IL-10 production from the transferred regulatory population to the host-derived, endogenously primed repertoire. Thus, our data provide a rationale for cell-based therapeutic intervention in multiple sclerosis by showing that pre-emptive targeting of the epitope spreading cascade with regulatory T cells effectively induces an immune-deviated spreading response capable of inhibiting ongoing inﬂammatory autoreactivity and disease progression. The Journal of Immunology, 2001, 167: 6105–6112. relapse, proliferative responses, and cytokine responses of treatment groups were compared using repeated measures ANOVA. Outcome differences for overall signiﬁcance were de- termined by the Tukey-Kramer multiple comparison procedure. Differences in PLP immunostaining of spinal cord sections were determined by the unpaired Student t test.
Size-Dependent Antimicrobial Effects of Novel Palladium Nanoparticles

Investigating the interactions between nanoscale materials and microorganisms is crucial to provide a comprehensive, proactive understanding of nanomaterial toxicity and explore the potential for novel applications. It is well known that nanomaterial behavior is governed by the size and composition of the particles, though the effects of small differences in size toward biological cells have not been well investigated. Palladium nanoparticles (Pd NPs) have gained significant interest as catalysts for important carbon-carbon and carbon-heteroatom reactions and are increasingly used in the chemical industry, however, few other applications of Pd NPs have been investigated. In the present study, we examined the antimicrobial capacity of Pd NPs, which provides both an indication of their usefulness as target antimicrobial compounds, as well as their potency as potential environmental pollutants. We synthesized Pd NPs of three different well-constrained sizes, 2.0±0.1 nm, 2.5±0.2 nm and 3.1±0.2 nm. We examined the inhibitory effects of the Pd NPs and Pd2+ ions toward gram negative Escherichia coli (E. coli) and gram positive Staphylococcus aureus (S. aureus) bacterial cultures throughout a 24 hour period. Inhibitory growth effects of six concentrations of Pd NPs and Pd2+ ions (2.5×10−4, 10−5, 10−6, 10−7, 10−8, and 10−9 M) were examined. Our results indicate that Pd NPs are generally much more inhibitory toward S. aureus than toward E. coli, though all sizes are toxic at ≥10−5 M to both organisms. We observed a significant difference in size-dependence of antimicrobial activity, which differed based on the microorganism tested. Our work shows that Pd NPs are highly antimicrobial, and that fine-scale (<1 nm) differences in size can alter antimicrobial activity.
MAX: human-centric search of the physical world

MAX is a system that facilitates human-centric search of the physical world. It allows humans to search for and locate objects as and when they need it instead of organizing them a priori. It provides location information in a form natural to humans, i.e., with reference to identifiable landmarks (e.g., on the dining table) rather than precise coordinates. MAX was designed with the following objectives: (i) human-centric operation, (ii) privacy, and (iii) efficient search of any tagged object. In the system, all physical objects, from documents to clothing, can be tagged and people locate objects using an intuitive search interface. To make search efficient, MAX adopts a hierarchical architecture consisting of tags (bound to objects), sub-stations (bound to landmarks) and base-stations (bound to localities). Tags can be marked as either public or private, with private tags searchable only by the owner. MAX also provides for privacy of physical spaces.MAX requires minimal initial configuration, and is robust to reconfiguration of the physical space. To optimize system performance, we present a methodology to design energy and delay optimal query protocols for a variety of device choices. We have implemented MAX using Crossbow motes and conducted user trials in a 5m by 5m cluttered office. The user feedback was positive, demonstrating the feasibility of MAX for human-centric search. We contend that a MAX-like search system will enable sharing (e.g., books on a college campus) and trading (e.g., buying and selling used books) of physical resources, and will be the engine for a host of new applications.
Intermetallic compound identification and Kirkendall void formation in eutectic SnIn/Cu solder joint during solid-state aging

Microstructural investigations were performed on the interfacial reactions between eutectic SnIn solder and Cu substrate during reflowing at 433 K and solid-state aging at 373 K. Cu2(In,Sn) was identified as the only intermetallic compound (IMC) at the interface, which consists of two sublayers with different morphology, a fine-grained sublayer at the Cu side and a coarse-grained sublayer at the solder side. During solid-state aging, voids were found between these two Cu2(In,Sn) sublayers but not at the substrate interface, which is also attributed to the Kirkendall effect considering the different diffusion fluxes of Sn or In and Cu atoms in different sublayers.
Integrated Whole Genome and Transcriptome Analysis Identified a Therapeutic Minor Histocompatibility Antigen in a Splice Variant of ITGB2

Purpose: In HLA-matched allogeneic hematopoietic stem cell transplantation (alloSCT), donor T cells recognizing minor histocompatibility antigens (MiHAs) can mediate desired antitumor immunity as well as undesired side effects. MiHAs with hematopoiesis-restricted expression are relevant targets to augment antitumor immunity after alloSCT without side effects. To identify therapeutic MiHAs, we analyzed the in vivo immune response in a patient with strong antitumor immunity after alloSCT. Experimental Design: T-cell clones recognizing patient, but not donor, hematopoietic cells were selected for MiHA discovery by whole genome association scanning. RNA-sequence data from the GEUVADIS project were analyzed to investigate alternative transcripts, and expression patterns were determined by microarray analysis and qPCR. T-cell reactivity was measured by cytokine release and cytotoxicity. Results: T-cell clones were isolated for two HLA-B*15:01–restricted MiHA. LB-GLE1-1V is encoded by a nonsynonymous SNP in exon 6 of GLE1. For the other MiHAs, an associating SNP in intron 3 of ITGB2 was found, but no SNP disparity was present in the normal gene transcript between patient and donor. RNA-sequence analysis identified an alternative ITGB2 transcript containing part of intron 3. qPCR demonstrated that this transcript is restricted to hematopoietic cells and SNP-positive individuals. In silico translation revealed LB-ITGB2-1 as HLA-B*15:01–binding peptide, which was validated as hematopoietic MiHA by T-cell experiments. Conclusions: Whole genome and transcriptome analysis identified LB-ITGB2-1 as MiHAs encoded by an alternative transcript. Our data support the therapeutic relevance of LB-ITGB2-1 and illustrate the value of RNA-sequence analysis for discovery of immune targets encoded by alternative transcripts. Clin Cancer Res; 22(16); 4185–96. ©2016 AACR.
Semantic Analysis for Keywords Based User Segmentation from Internet Data

Nowadays, Internet has been one of the major advertising channels and behavioral targeting has become increasingly important for improving the click-through rate of online advertisements. One of the key research problems in behavioral targeting is how to group users into segments with similar interests or backgrounds. In this paper, we propose a web page-oriented and keywords-based approach to address this problem. Our approach includes two key components: keyword similarity measurement and keyword similarity based user segmentation. These two components serve as plugins and can be replaced with better algorithms or measurements, making our approach very flexible. We have implemented the first key component, and provide preliminary results to illustrate the effectiveness of this component in finding similar news pages based on their keywords.
Pathophysiological Responses to Acute Cerebral Ischemia in the Gerbil

The left carotid artery of healthy, male gerbils was surgically ligated to induce a state of cerebral ischemia. The animals were sacrificed two, four, six, 12, 24 and 48 hours postligation to determine whether the induced cerebral ischemia would be reflected by changes in blood chemistry. The gerbil, unlike the rat, has a well-defined circle of Willis and cerebral arterial branches which resemble the arrangement of cerebral arteries found in man. The gerbils withstood the induced cerebral ischemia relatively well with few overt signs of cerebral damage, e.g., muscular paralysis, and a low mortality rate. However, intense lipid mobilization accompanied by depletion of peripheral adipose tissue sites and fatty infiltration of the liver developed very promptly. Marked cerebral edema and definitive foci of cerebral infarction occurred in both the frontal and medial lobes of the brain. The adrenal cortices of the gerbil were markedly depleted of lipid concomitant with severe thymus gland involution indicative of intense corticosteroid release. The serum enzymes, creatine phosphokinase and glutamic oxaloacetic transaminase, both rose promptly, indicating cerebral and hepatic damage respectively. Lipids, i.e., triglycerides, free fatty acids and total cholesterol, all rose promptly and to significantly above-normal levels and remained super-normal throughout the 48-hour course of the experiment. Concomitant with the hyperlipidemia and other metabolic changes there were definite hyperglycemia and elevation of BUN levels in a brisk response to the induced, acute cerebral ischemia. The gerbil adrenal gland produces hydrocortisone predominantly. Blood levels of hydrocortisone rose quickly to super-normal levels in response to the stress of cerebral ischemia but fell to significantly below-normal levels 24 and 48 hours after carotid artery ligation. These findings demonstrate that acute cerebral ischemia constitutes a severe stress in the gerbil which is reflected, almost quantitatively, by temporal changes in such blood constituents as enzymes, lipids, glucose, and adrenal stress hormones.
Aortic Regurgitation and Left Ventricular Remodeling After Transcatheter Aortic Valve Implantation: A Serial Cardiac Magnetic Resonance Imaging Study

Background—Aortic regurgitation (AR) after transcatheter aortic valve implantation (TAVI) has been associated with poor outcomes, but little is known about how it evolves over time. We evaluated left ventricular (LV) function, remodeling, and the occurrence and evolution of AR after TAVI by using cardiac MRI. Methods and Results—Forty-three patients treated with transfemoral TAVI underwent cardiac MRI 1 week and 6 months after TAVI. LV volumes and function were assessed by using standard cine MRI sequences. Phase-contrast imaging was performed to quantify the degree of AR. The mean age of the evaluated patients was 80 years, and 65% of patients were women. At baseline MRI, the median LV ejection fraction was 58.1%, which improved significantly at follow-up to 63.4% (P<0.0001). A significant reduction of LV end-diastolic volume (149.7±41.4–140.1±43.9 mL; P=0.014) and of LV mass (156.3±32.8–142.7±39.3 g; P<0.001) was observed. Over time, aortic regurgitant fraction increased slightly but significantly from 5.2% to 7.8% (P=0.04). Subgroup analysis revealed that significant changes of LV ejection fraction, volumes, and mass only occurred in patients with no or mild AR at baseline MRI, whereas those parameters remained unchanged in patients with AR more than or equal to grade II. Conclusions—By using cardiac MRI in patients with TAVI, a significant improvement of LV function, volume, and mass can be documented. Mild-to-moderate AR is commonly seen, and AR shows a small increase over time. More-than-mild AR seems to prevent LV functional and structural recovery after TAVI.
Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire

Antibody repertoire diversity, potentially as high as 1011 unique molecules in a single individual, confounds characterization by conventional sequence analyses. In this study, we present a general method for assessing human antibody sequence diversity displayed on phage using massively parallel pyrosequencing, a novel application of Kabat column-labeled profile Hidden Markov Models, and translated complementarity determining region (CDR) capture-recapture analysis. Pyrosequencing of domain amplicon and RCA PCR products generated 1.5 × 106 reads, including more than 1.9 × 105 high quality, full-length sequences of antibody variable fragment (Fv) variable domains. Novel methods for germline and CDR classification and fine characterization of sequence diversity in the 6 CDRs are presented. Diverse germline contributions to the repertoire with random heavy and light chain pairing are observed. All germline families were found to be represented in 1.7 × 104 sequences obtained from repeated panning of the library. While the most variable CDR (CDR-H3) presents significant length and sequence variability, we find a substantial contribution to total diversity from somatically mutated germline encoded CDRs 1 and 2. Using a capture-recapture method, the total diversity of the antibody library obtained from a human donor Immunoglobulin M (IgM) pool was determined to be at least 3.5 × 1010. The results provide insights into the role of IgM diversification, display library construction, and productive germline usages in antibody libraries and the humoral repertoire.
Sicherheit und Privatsphäre in Online Sozialen Netzwerken

Online Soziale Netzwerke (OSNs) reprasentieren das vorherrschende Medium zur computergestutzten Kommunikation und Verbreitung personlicher, geschaftlicher oder auch wissenschaftlicher Inhalte. Eine Reihe von Vorkommnissen in der jungsten Vergangenheit hat gezeigt, dass die Bereitstellung privater Informationen in OSNs mit erheblichen Risiken fur die Sicherheit und den Schutz der Privatsphare seiner Nutzer verbunden ist. Gleiches gilt fur die Bereiche Wirtschaft und Wissenschaft. Ursachlich dafur ist die zentralisierte Verwaltung der Nutzer und ihrer publizierten Inhalte unter einer singularen administrativen Domane. Mit Vegas prasentiert der erste Teil dieser Arbeit ein dezentrales OSN, das mit seiner restriktiven Sicherheitsarchitektur diesem Problem begegnet. Oberstes Ziel ist die technische Umsetzung des Rechts auf informationelle Selbstbestimmung. Dazu schrankt Vegas den Zugriff auf den sozialen Graphen und jeglichen Informationsaustausch auf die Nutzer des eigenen Egonetzwerks ein. Neben der Moglichkeit zur Kommunikation und der Bereitstellung personlicher Informationen erlauben einige OSNs auch das Browsen des sozialen Graphen und die Suche nach Inhalten anderer Nutzer. Um auch in sicheren und die Privatsphare schutzenden OSNs wie Vegas vom akkumulierten Wissen des sozialen Graphen zu profitieren, beschaftigt sich der zweite Teil dieser Arbeit mit der Entwicklung und Analyse intelligenter Priorisierungsstrategien zur Weiterleitung von Suchanfragen innerhalb dezentraler OSNs. Im Kontext von OSNs werden neue Algorithmen und Protokolle zunachst simulativ evaluiert. Die Grundlage bildet in der Regel der Crawling-Datensatz eines OSNs. Offensichtlich ist das Crawling in sicheren und die Privatsphare schutzenden dezentralen OSNs wie Vegas nicht moglich. Um diesem Problem zu begegnen, beschaftigt sich der dritte Teil dieser Arbeit mit der Entwicklung eines generischen Modells zur kunstlichen Erzeugung sozialer Interaktionsgraphen. Neben den strukturellen Besonderheiten zentralisierter und dezentraler Systeme wird erstmals auch das Interaktionsverhalten der Nutzer eines OSNs modelliert. Die Eignung des Modells wird auf der Grundlage gecrawlter sozialer Graphen evaluiert.
The Implementation of SLA Mechanism in Manufacturing Grid

In MG environment, resource consumers choose the optimal resource service according to their non-functional demands for quality of service (QoS) in terms of service execution time, reliability, and availability. Non-functional requirements of QoS can be organized and managed by utilizing Service Level Agreement (SLA) standards. In this study, architectures with QoS oriented mechanism with four layers for MG on the basis of SLA are provided. On the basis of the QoS oriented architectures, the management processes of SLA creation, negotiation and matching, monitoring and verification are discussed. Finally, a simple case is provided.
Exercise and Respiratory Training Improve Exercise Capacity and Quality of Life in Patients With Severe Chronic Pulmonary Hypertension

Background— Pulmonary hypertension (PH) is associated with restricted physical capacity, limited quality of life, and a poor prognosis because of right heart failure. The present study is the first prospective randomized study to evaluate the effects of exercise and respiratory training in patients with severe symptomatic PH. Methods and Results— Thirty patients with PH (21 women; mean age, 50±13 years; mean pulmonary artery pressure, 50±15 mm Hg; mean World Health Organization [WHO] class, 2.9±0.5; pulmonary arterial hypertension, n=23; chronic thromboembolic PH, n=7) on stable disease-targeted medication were randomly assigned to a control (n=15) and a primary training (n=15) group. Medication remained unchanged during the study period. Primary end points were the changes from baseline to week 15 in the distance walked in 6 minutes and in scores of the Short Form Health Survey quality-of-life questionnaire. Changes in WHO functional class, Borg scale, and parameters of echocardiography and gas exchange also were assessed. At week 15, patients in the primary and secondary training groups had an improved 6-minute walking distance; the mean difference between the control and the primary training group was 111 m (95% confidence interval, 65 to 139 m; P<0.001). Exercise training was well tolerated and improved scores of quality of life, WHO functional class, peak oxygen consumption, oxygen consumption at the anaerobic threshold, and achieved workload. Systolic pulmonary artery pressure values at rest did not change significantly after 15 weeks of exercise and respiratory training (from 61±18 to 54±18 mm Hg) within the training group. Conclusions— This study indicates that respiratory and physical training could be a promising adjunct to medical treatment in severe PH. The effects add to the beneficial results of modern medical treatment.
A New Approach for Touching Cells Segmentation

Automatic cell segmentation has various applications in different parts of science. The development of automated methods for cell segmentation, remains challenging in situations where there are touching cells. In this paper we propose a new method for separating touching cells. As the first step, we use a combination of graph segmentation algorithm and thresholding for segmenting foreground objects and producing a binary image. Next, boundary points of separation zone are selected by using a corner detection algorithm. Finally, the marker controller watershed transform is applied to separate touching cells at selected points.
RNA silencing in surgical disease.

Each of our cells contains a complete copy of the genes required to create a whole organism. Thus, it was possible to clone Dolly from a single sheep epidermal cell, and we should be able to reconstruct a dinosaur from the genetic material buried in the mud of Jurassic Park. However, it is hard to believe that by adding water to the $5 worth of chemicals in a human, it is possible to create a human being. Although 30000 instructions, or genes, sounds like a lot, the creation of a hand or a heart or a mind is still a daunting task. Our current genetic code is a lot like the King James Bible-both have evolved. The travails of Moses or Noah were initially transcribed by clerics into huge books safely stored in cathedral vaults. With frightening frequency, these imaginative priests improved the story as they wrote. The testaments were then translated into many languages to enhance access by many peoples. These translations were found, and the data enjoyed further incremental evolution. In eukaryotes, the functional DNA rarely leaves the safety of the nuclear cathedral vault. Traditionally, we have envisioned the Gideon messengers as transcribing reliable molecular copies and distributing them out to motel rooms. While chromosomes are made of double-stranded DNA comprising millions of nucleotide pairs, single-strand messenger RNA (mRNA) carries only single verses, requiring a nucleotide code of only 50 to several thousand nucleotides. Ribosomal RNA synthesizes protein from the mRNA script, while transfer RNA serves an adaptor role in converting the message to protein.
Small fiber neuropathy is a common feature of Ehlers-Danlos syndromes

Objective: To investigate the involvement of small nerve fibers in Ehlers-Danlos syndrome (EDS). Methods: Patients diagnosed with EDS underwent clinical, neurophysiologic, and skin biopsy assessment. We recorded sensory symptoms and signs and evaluated presence and severity of neuropathic pain according to the Douleur Neuropathique 4 (DN4) and ID Pain questionnaires and the Numeric Rating Scale (NRS). Sensory action potential amplitude and conduction velocity of sural nerve was recorded. Skin biopsy was performed at distal leg and intraepidermal nerve fiber density (IENFD) obtained and referred to published sex- and age-adjusted normative reference values. Results: Our cohort included 20 adults with joint hypermobility syndrome/hypermobility EDS, 3 patients with vascular EDS, and 1 patient with classic EDS. All except one patient had neuropathic pain according to DN4 and ID Pain questionnaires and reported 7 or more symptoms at the Small Fiber Neuropathy Symptoms Inventory Questionnaire. Pain intensity was moderate (NRS ≥4 and <7) in 8 patients and severe (NRS ≥7) in 11 patients. Sural nerve conduction study was normal in all patients. All patients showed a decrease of IENFD consistent with the diagnosis of small fiber neuropathy (SFN), regardless of the EDS type. Conclusions: SFN is a common feature in adults with EDS. Skin biopsy could be considered an additional diagnostic tool to investigate pain manifestations in EDS.
A simple layered RGB BRDF model

Many natural objects, and general layered materials, have non-linear reflection behaviour along wavelengths. An accurate representation of phenomena such as interference and colour separation generally requires a fine spectral representation of light instead of the commonly used RGB components. In this article, we introduce and experiment with a general approach to create similar and convincing effects, with a simple RGB BRDF model. We present a model for both specular and diffuse reflection.