Miracle-dz/UniFAR-FTUs huggingface dataset:
Directed evolution of human T cell receptor CDR2 residues by phage display dramatically enhances affinity for cognate peptide‐MHC without increasing apparent cross‐reactivity

The mammalian α/β T cell receptor (TCR) repertoire plays a pivotal role in adaptive immunity by recognizing short, processed, peptide antigens bound in the context of a highly diverse family of cell‐surface major histocompatibility complexes (pMHCs). Despite the extensive TCR–MHC interaction surface, peptide‐independent cross‐reactivity of native TCRs is generally avoided through cell‐mediated selection of molecules with low inherent affinity for MHC. Here we show that, contrary to expectations, the germ line‐encoded complementarity determining regions (CDRs) of human TCRs, namely the CDR2s, which appear to contact only the MHC surface and not the bound peptide, can be engineered to yield soluble low nanomolar affinity ligands that retain a surprisingly high degree of specificity for the cognate pMHC target. Structural investigation of one such CDR2 mutant implicates shape complementarity of the mutant CDR2 contact interfaces as being a key determinant of the increased affinity. Our results suggest that manipulation of germ line CDR2 loops may provide a useful route to the production of high‐affinity TCRs with therapeutic and diagnostic potential.
Ultrasound Evaluation of Adnexal Pathologies

The objective of the study was to evaluate the role of ultrasound in diagnosis of adnexal pathologies. The ultrasound findings were correlated with per-operative & histo-pathological findings. The study was prospective and was carried out between March 2014 to August 2014 at the Department of Radiology, P.D. U. Govt. Medical College and Civil Hospital, Rajkot. Abdominal ultrasound & Doppler study with clinical & pathological correlation of 50 cases was done for diagnosing adnexal pathologies accurately. Out of 50 patients diagnosed by ultrasound, the most common adnexal lesions seen in our study were- simple cyst, complex cyst, hemorrhagic cyst, Hydrosalpinx, dermoids, tubo- ovarian abscess, polycystic ovarian disease, endometrioma, cystadenomas, malignant masses, torsion of ovary & ectopic pregnancy. The diagnosis given on ultrasound & Doppler was confirmed with per-op & histo-pathological findings. Pelvic ultrasound is commonly used to evaluate adnexal masses, it is important to understand the most useful sonographic features for predicting benign and malignant masses. Determining whether an adnexal mass is of ovarian or extra ovarian origin is key in arriving at the most likely diagnosis. Most adnexal masses are benign, and each of the most common benign ovarian lesions has a typical sonographic appearance. Additionally, most malignant ovarian neoplasms have a solid component with detectable flow by Doppler ultrasound, allowing one to strongly suggest the diagnosis.
Diversité des arbres et résistance des forêts aux invasions biologiques : application au chataignier et son complexe de bioagresseurs exotiques, chancre (Cryphonectria parasitica) et cynips (Dryocosmus Kuriphilus)

Les plantes sont au centre d’une grande diversite d’interactions biotiques entre organismes plus ou moins proches qui les exploitent en tant que ressources. L’objectif de cette these a ete de comprendre comment les infections fongiques de la plante et la diversite des arbres en foret modifient les interactions arbres-insectes. Nous avons tout d’abord effectue une meta-analyse pour poser le cadre theorique des effets indirects des infections fongiques sur les insectes herbivores associes aux memes plantes hotes. L'effet de l’infection prealable des plantes par les champignons sur les preferences et performances des insectes s’avere generalement negatif. Cependant, la magnitude de cet effet deletere varie selon le mode de vie du champignon, la guilde trophique de l’insecte et la spatialite des interactions (interactions locales vs distantes). Nous avons ensuite analyse de facon empirique les interactions tripartites entre le châtaignier europeen (Castanea sativa) et deux de ses bioagresseurs exotiques: le cynips (Dryocosmus kuriphilus), insecte galligene, et Cryphonectria parasitica, champignon pathogene responsable de la maladie du chancre. L'effet sur les taux d’infestation par le cynips de la composition specifique en essences forestieres des forets de châtaigniers atteintes de chancre a ete egalement etudie. Afin d'identifier les mecanismes sous-jacents aux effets de la diversite des forets sur cet insecte invasif, les communautes d'insectes parasitoides et de champignons endophytes presents dans les galles ont ete decrites. Les taux d’infection par le cynips etaient plus faibles dans les melanges de châtaignier avec du chene et du frene que dans des parcelles de châtaignier monospecifiques ou dans les melanges avec du pin. La composition des forets influence aussi la composition des communautes de parasitoides associes aux galles du cynips mais pas leur abondance, richesse ou diversite. Les communautes de champignons endophytes des galles, etudiees par des methodes de sequencage de nouvelle generation, sont independantes de la composition forestiere. Par contre, celles presentes dans les galles different fortement de celles des tissus foliaires adjacents. Nous avons ainsi apporte de nouvelles preuves que la diversite des plantes et les champignons pathogenes sont des facteurs cles determinant les interactions plantes-insectes. Etudier comment les plantes interagissent avec leurs insectes et champignons associes, et les mecanismes sous-jacents a l’effet de la diversite des plantes sur ces interactions, doit permettre de mieux comprendre les relations entre diversite et fonctionnement des ecosystemes et de proposer des applications pour la gestion des bio-agresseurs forestiers natifs et exotiques.
The Open Artery Hypothesis: Beneficial Effects and Long-term Prognostic Importance of Patency of the Infarct-Related Coronary Artery

There seem to be additional mechanisms of benefit in patients receiving late reperfusion therapy in a time when the opportunity for myocardial salvage has been missed. Previous studies have demonstrated that the restoration of blood flow in the infarct-related coronary artery in patients with acute myocardial infarction improves left ventricular function and reduces mortality. Initially, it was thought that survival was improved because viable myocardium was salvaged. However, data obtained over the past several years have suggested that the restoration of antegrade flow in the infarct-related artery may improve survival via a mechanism independent of the influence on left ventricular function. Clinical interest in the open artery hypothesis has recently resurfaced owing to a substantial improvement in technical aspects of percutaneous coronary interventions (PCI). Observational data suggest a role for late intervention as safer and more effective mechanical reperfusion practices have emerged. Long-term clinical benefits have been shown from balloon angioplasty late after myocardial infarction (MI). Therefore, patients with failed thrombolysis or those with late-presenting MI may still benefit from PCI by mechanisms independent of myocardial salvage. There is accumulative evidence on this matter. Possible mechanisms include reduction of ventricular remodeling, diminished ventricular instability reducing the incidence of arrhythmias, and provision of collaterals to other territories in the event of further coronary artery occlusion. However, caution must be exercised in interpreting the results of studies examining the open artery hypothesis. This hypothesis can be tested in its purest sense in animal experiments; however, the clinical situation is much more complex. Patients may have acute-on-chronic coronary artery occlusion in the presence of multivessel disease and well-developed collateral channels. The pattern of necrosis may also be different with areas of necrosis separated by islands of ischemic, stunned, hibernating, or normal cells. Therefore, the patency of the infarct-related coronary artery in single or multivessel disease days to weeks after infarction markedly influences long-term prognosis unrelated to improvement of left ventricular function. Current technology has made it feasible to open and maintain patency of most occluded infarct-related arteries. However, the hypothesis that late mechanical reperfusion in patients with asymptomatic occluded infarct-related artery will improve long-term clinical outcomes remains to be proved and is currently being tested in a large randomized trial.
Elevated endothelin-1 (ET-1) levels may contribute to hypoadiponectinemia in childhood obesity.

CONTEXT Pediatric obesity is associated with endothelial dysfunction and hypoadiponectinemia, but the relationship between these two conditions remains to be fully clarified. Whether enhanced release of endothelin-1 (ET-1) may directly impair adiponectin (Ad) production in obese children is not known. OBJECTIVE The aim of the study was to explore whether and how high circulating levels of ET-1 may contribute to impair Ad production, release, and vascular activity. DESIGN AND PARTICIPANTS Sixty children were included into obese (Ob; n = 30), overweight (OW; n = 11), and lean (n = 19) groups. Total and high-molecular-weight Ad, ET-1, vascular cell adhesion molecule-1, and von Willebrand factor levels were measured in serum samples. Adipocytes were stimulated with exogenous ET-1 or with sera from lean, OW, and Ob, and Ad production and release measured in the absence or in the presence of ETA (BQ-123) and ETB (BQ-788) receptor blockers, p42/44 MAPK inhibitor PD-98059, or c-Jun NH2-terminal protein kinase inhibitor SP-600125. Vasodilation to Ad was evaluated in rat isolated arteries in the absence or in the presence of BQ-123/788. RESULTS Total and high-molecular-weight Ad was significantly decreased and ET-1 levels significantly increased in OW (P < .01) and Ob (P < .001) children. A statistically significant linear regression (P < .01) was found between Ad and ET-1. Exposure of adipocytes to exogenous ET-1 or serum from OW and Ob significantly decreased Ad mRNA and protein levels (P < 0.001). The inhibitory effect of ET-1 on Ad was reverted by BQ-123/788 or PD-98059 but not SP-600125. Ad-mediated vasodilation was further increased in arteries pretreated with BQ-123/788. CONCLUSIONS ET-1-mediated inhibition of Ad synthesis via p42/44 MAPK signaling may provide a possible explanation for hypoadiponectinemia in pediatric obesity and contribute to the development of cardiovascular complications.
Dynamic reconfiguration of Corba-based applications

Distributed applications are prone to drastic evolution during their lifetime due to user requirements, technological changes or modification of the execution environment. Application evolutions involve changes related to: (1) the application architecture, (2) the software implementation or (3) the physical location, of software components in a distributed environment during the application execution. Coping with such changes is recognized as being a difficult issue because new features must be integrated in existing applications at minimal cost and with minimal perturbation. We have designed an original algorithm for dynamic application reconfiguration, which fulfills the above requirements and we have implemented a prototype of this algorithm in a Corba environment. This prototype extends the current Corba programming model by introducing a framework for configurable object programming. The algorithm allows reconfiguration operations, such as the replacement, migration or dynamic rebinding of components. Our tools demonstrate that it is possible to reconfigure an application with minimal perturbation.
British library and information science journals: a study of quality control

Assessment of the quality of published research is funda mental to the research assessment process in UK universi ties. Citation analysis has been one important method used for such assessment. This paper explores another method, by investigating the selection and refereeing processes used by journal editors. Starting from the journals in which UK LIS academics most frequently publish, the authors have described and analysed the editorial processes employed, drawing on extended interviews with editors and others. It is concluded that valid quality control mechanisms are in place, although there is an element of subjectivity in their application, and it is suggested that professional, as opposed to academic, journals can provide a valuable form of output for practice-oriented research findings. Finally, the authors note that electronic journals could be assessed by a methodology similar to that developed here.
A multiple-syringe bacteriophage applicator.

Bacteriophage typing of Staphylococci is a laborious, repetitive, time-consuming technic. Some relief has been realized through the development of the lyophilization procedure, eliminating the need for almost continuous virus propagation, a technic requiring a high degree of skill and knowledge of virology. Assuming the use of lyophilized phage, the most time-consuming facet of phage typing is the individual dropping of each of 20 or more phages onto the staphylococcal "lawn" in each of a series of individual petri plates. In order to meet the problem in this laboratory, a machine has been devised that dispenses up to 26 phage types very accurately and rapidly to 160 plates with 1 filling. Upkeep is negligible; cleaning, sterilizing, and filling are simplei to perform. In order to meet the need for bacteriophage-typing of large numbers of Staphylococcus aureus typing isolations, numerous devices for the multiple application of phage suspensions have been described. Goldberg and Steers and co-workers have described devices using the replication principle of Lederberg and Lederberg. These consist of a block of rods that are dipped into the phage suspensions in a cup plate and the adhering liquid applied to sterile agar in petri plates. After absorption of the droplets (containing the phage) into the agar, the plates are then flooded with 1 ml. of a broth culture of the organism to be typed. The petri plates are then slanted and the excess removed by means of a pipet. Tarr devised a multiple-loop arrangement for applying the suspensions of bacteriophage. Lidwell refined this method by
Catalysis at the Origin of Life Viewed in the Light of the ( M , R )-Systems of Robert

Living systems as we know them today are both complex, displaying emergent properties, and extremely complicated, with huge numbers of different components. At the origin of life they must also have had emergent properties, and hence must have been complex, but they cannot have been as complicated as modern organisms, because we cannot imagine that the first organisms started with anything as elaborate as a ribosome and all of the protein-synthesis machinery. Understanding how complexity could arise in even the simplest early organism requires, however, a theory of life, something that is largely lacking from modern biology. Various authors have contributed elements of such a theory, and the (M,R)-systems of Robert Rosen provide a convenient starting point.
Staphylococcal biofilm formation as affected by type acidulant

Staphylococcal growth and biofilm formation in culture medium where pH was lowered with weak organic (acetic and lactic) or strong inorganic (hydrochloric) acids were studied. The effects were evaluated by biomass measurements, cell‐surface hydrophobicity, scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM). The results demonstrated that the inhibition was related to type of acidulant and pH value. At pH 5.0, the antibacterial effect was more pronounced in the presence of acetic acid (58–60% growth reduction) compared with that in the presence of lactic (7–16% growth reduction) and hydrochloric acids (23–24% reduction). The biofilm biomass of Staphylococcus aureus and Staphylococcus epidermidis was reduced by 92, 85, 63, and 93, 87, 81% after exposition to acetic, lactic, and hydrochloric acids, respectively. Increasing the pH from 5.0 to 6.0 resulted in a noticeable reduction in the effectiveness of acids. A minor cells hydrophobic character was also documented. The SEM and CLSM revealed a poorly structured and thinner biofilm compared with the dense and multilayered control. Acidic environment could have important implications for food‐processing system to prevent bacterial colonization and control biofilm formation. The findings of this study lead to consider the rational use of the type of acid to achieve acidic environments.
Learning to avoid spiders: fear predicts performance, not competence

ABSTRACT We used an immersive virtual environment to examine avoidance learning in spider-fearful participants. In 3 experiments, participants were asked to repeatedly lift one of 3 virtual boxes, under which either a toy car or a spider appeared and then approached the participant. Participants were not told that the probability of encountering a spider differed across boxes. When the difference was large (Exps. 1 and 2), spider-fearfuls learned to avoid spiders by lifting the few-spiders-box more often and the many-spiders-box less often than non-fearful controls did. However, they hardly managed to do so when the probability differences were small (Exp. 3), and they did not escape from threat more quickly (Exp. 2). In contrast to the observed performance differences, spider-fearfuls and non-fearfuls showed equal competence, that is comparable post-experimental knowledge about the probability to encounter spiders under the 3 boxes. The limitations and implications of the present study are discussed.
The Requirement for Potent Adjuvants To Enhance the Immunogenicity and Protective Efficacy of Protein Vaccines Can Be Overcome by Prior Immunization with a Recombinant Adenovirus

A central goal in vaccinology is the induction of high and sustained Ab responses. Protein-in-adjuvant formulations are commonly used to achieve such responses. However, their clinical development can be limited by the reactogenicity of some of the most potent preclinical adjuvants and the cost and complexity of licensing new adjuvants for human use. Also, few adjuvants induce strong cellular immunity, which is important for protection against many diseases, such as malaria. We compared classical adjuvants such as aluminum hydroxide to new preclinical adjuvants and adjuvants in clinical development, such as Abisco 100, CoVaccine HT, Montanide ISA720, and stable emulsion-glucopyranosyl lipid A, for their ability to induce high and sustained Ab responses and T cell responses. These adjuvants induced a broad range of Ab responses when used in a three-shot protein-in-adjuvant regimen using the model Ag OVA and leading blood-stage malaria vaccine candidate Ags. Surprisingly, this range of Ab immunogenicity was greatly reduced when a protein-in-adjuvant vaccine was used to boost Ab responses primed by a human adenovirus serotype 5 vaccine recombinant for the same Ag. This human adenovirus serotype 5–protein regimen also induced a more cytophilic Ab response and demonstrated improved efficacy of merozoite surface protein-1 protein vaccines against a Plasmodium yoelii blood-stage challenge. This indicates that the differential immunogenicity of protein vaccine adjuvants may be largely overcome by prior immunization with recombinant adenovirus, especially for adjuvants that are traditionally considered poorly immunogenic in the context of subunit vaccination and may circumvent the need for more potent chemical adjuvants.
A Two-Stage Manifold Learning Framework for Machinery Fault Diagnosis

This study presents a new fault diagnosis method based on a two-stage manifold learning framework to further improve fault diagnosis accuracy. First of all, nonlinear de-noising method with unsupervised manifold learning is presented, by combining advantages of manifold learning in mining of nonlinear structure and phase space reconstruction in representation of signal and noise spatial distribution. Then, the frequency spectrum of vibration signals after de-noising is used for fault feature extraction. In order to reduce the high dimensionality and remove redundant information of frequency spectrum, an improved supervised local tangent space alignment (ISLTSA) is proposed. ISLTSA further increases interclass distance and further reduces intraclass distance, and as a result the extracted fault features are more identifiable. At last, the extracted low-dimensional fault features are inputted into a pattern recognition method for fault identification. A fault diagnosis case in bearings is studied to verify the effectiveness of the proposed method.
Comparative analysis of rotor losses in high-speed permanent magnet machines with different winding configurations considering the influence of the inverter PWM

Due to development in fields of materials and power electronics, use of high-speed electrical machines has boosted significantly in recent decades. They are widely used in number of applications, such as electrically assisted turbochargers, flywheel energy storage systems, spindle applications, turbo molecular pumps, micro gas turbines. In applications where high efficiency and high power density are required, the most suitable machine type for high-speed operations is a permanent magnet (PM) machine. In this paper the performance of several different topologies of high-speed PM machines required for use in a micro-gas turbine application are evaluated. Different winding topologies, retaining sleeve materials and magnetization patterns are considered, where the main criterion for the machine performance are eddy current losses in the rotor. Influence of time harmonics in stator currents caused by the inverter Pulse Width Modulation (PWM) is incorporated in the calculation.
Psychological Risk Factors and Self-Mutilation in Male Patients with Bpd *

The purpose of this study was to determine whether or not self-mutilation in patients with personality disorders is related to other psychological risk factors, dissociation or diagnosis. The sample included 61 subjects with borderline personality disorder and 60 subjects with nonborderline personality disorder; 32 subjects with borderline personality disorder reported self-mutilation. Psychological risk factors were measured through histories of childhood sexual abuse, physical abuse and separation or loss as well as through scores on the Parental Bonding Index. Dissociation was measured by the Dissociative Experiences Scale. There were no relationships between any of the psychological risk factors and self-mutilation. Subjects who mutilated themselves had higher scores on the Dissociative Experiences Scale in univariate analysis but the scores in multivariate analyses dissociation did not discriminate between subjects who mutilated themselves and those who did not. The results do not support the theory that abuse and dissociation account for self-mutilation in the personality disorders.