gebhart/patrepeval huggingface dataset:
A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees (2008)

This is the first study that estimates mycobacterial phylogeny using the maximum-likelihood method (PhyML-aLRT) on a seven-gene concatenate (hsp65, rpoB, 16S rRNA, smpB, sodA, tmRNA and tuf) and the super distance matrix (SDM) supertree method. Two sets of sequences were studied: a complete seven gene sequence set (set R, type strains of 87 species) and an incomplete set (set W, 132 species) with some missing data. Congruencies were computed by using the consense program (phylip package). The evolution rate of each gene was determined, as was the evolution rate of each strain for a given gene. Maximum-likelihood trees resulting from concatenation of the R and W sets resulted in a similar phylogeny, usually showing an early separation between slow-growing (SG) and rapidly growing (RG) mycobacteria. The SDM tree for the W set resulted in a different phylogeny. The separation of SG and RG was still evident, but it was located later in the nodes. The SG were therefore positioned as a subgroup of RG. Maximum-likelihood phylogenetic reconstruction was less affected by increasing the number of strains (with incomplete data), but did seem to cushion the variability of the evolution rate (ER), whereas the SDM method seemed to be more accurate and took into account both the differing ER values and the incomplete data. With regard to ER, it was observed that the 16S rRNA gene was the gene that displayed the slowest evolution, whereas smpB was the most rapidly evolving gene. Surprisingly, these two genes alone accurately separated the SG from the RG on the basis of their ER values. This study focused on the differences in ER between genes and in some cases linked the ER to the phenotypic classification of the mycobacteria.
Intraoperative Image-based Multiview 2D/3D Registration for Image-Guided Orthopaedic Surgery: Incorporation of Fiducial-Based C-Arm Tracking and GPU-Acceleration (2011)

Intraoperative patient registration may significantly affect the outcome of image-guided surgery (IGS). Image-based registration approaches have several advantages over the currently dominant point-based direct contact methods and are used in some industry solutions in image-guided radiation therapy with fixed X-ray gantries. However, technical challenges including geometric calibration and computational cost have precluded their use with mobile C-arms for IGS. We propose a 2D/3D registration framework for intraoperative patient registration using a conventional mobile X-ray imager combining fiducial-based C-arm tracking and graphics processing unit (GPU)-acceleration. The two-stage framework 1) acquires X-ray images and estimates relative pose between the images using a custom-made in-image fiducial, and 2) estimates the patient pose using intensity-based 2D/3D registration. Experimental validations using a publicly available gold standard dataset, a plastic bone phantom and cadaveric specimens have been conducted. The mean target registration error (mTRE) was 0.34 ± 0.04 mm (success rate: 100%, registration time: 14.2 s) for the phantom with two images 90° apart, and 0.99 ± 0.41 mm (81%, 16.3 s) for the cadaveric specimen with images 58.5° apart. The experimental results showed the feasibility of the proposed registration framework as a practical alternative for IGS routines.
Multidrug resistance-associated protein 3 is a tumor rejection antigen recognized by HLA-A2402-restricted cytotoxic T lymphocytes. (2001)

The identification of tumor rejection antigens recognized by CTLs and its application in peptide-based specific immunotherapy against melanomas have been extensively investigated in the past decade. However, only a small number of studies regarding these issues in other epithelial cancers have been reported. In this study, we show that a multidrug resistance-associated protein 3 (MRP3) is a tumor rejection antigen recognized by HLA-A2402-restricted CTLs established from T cells infiltrating into lung adenocarcinoma. MRP3 is expressed in differing quantities in tumor cells of various tissue types and origins. Four dominant MRP3-derived antigenic peptides that are recognized by the CTLs have been identified, each possessing in vitro immunogenicity. Namely, these four peptides (MRP3-503, MRP3-692, MRP3-765, and MRP3-1293) can induce peptide-specific CTLs after in vitro stimulation with these peptides in peripheral blood mononuclear cell cultures of HLA-A24(+) cancer patients, with the CTLs expressing cytotoxicity against HLA-A2402(+) MRP3(+) tumor cells but not against either HLA-A2402(-) or MRP3(-) target cells. The peptide specificity of the cytotoxicity of the CTLs was further confirmed by using peptide-loaded HLA-A24(+) EBV-transformed B cells. Widespread MRP3 expression in various tumor cell lines and tumor tissues at the mRNA level was confirmed. Furthermore, reactivities of the MRP3-peptide-induced CTLs against tumor cells correlated with MRP3 expression in the tumor cells. These results suggest that MRP3 and its derived peptides described in the present paper are potential candidates for cancer vaccines in regard to HLA-A24(+) patients with various tumors, particularly for those tumors that show anticancer drug resistance.
“Decoy” of androgen‐responsive element induces apoptosis in LNCaP cells (1999)

BACKGROUND In an androgen-dependent manner, the androgen receptor (AR) binds to the androgen-responsive element (ARE) in the regulatory region of target genes. We hypothesize that an “ARE decoy,” a double-stranded oligonucleotide containing the same DNA sequence as ARE, can inhibit prostatic proliferation by competitive inhibition of AR transcriptional activity. METHODS We synthesized a 23-mer ARE decoy based on the deduced ARE sequence at the promoter region of the human prostate-specific antigen (PSA) gene. The nuclear extract was prepared from LNCaP cells, and DNA-protein interactions were examined by gel shift assay. Then the antiandrogen effect of the ARE decoy was studied in LNCaP cells transfected with the ARE decoy by lipofection. After 24-hr incubation with 10−9 M dihydrotestosterone (DHT), induction of apoptosis was examined by DNA fragmentation. RESULTS The gel shift assay demonstrated specific binding of the ARE decoy to the LNCaP nuclear protein which is most likely AR. The transfection experiment showed DNA fragmentation in the ARE decoy-transfected cells despite the presence of DHT, though not in the cells transfected with the control decoy. CONCLUSIONS The ARE decoy had an antiandrogen effect and induced apoptosis in LNCaP cells. This ARE decoy may become a potential therapeutic tool for prostate cancers when combined with a highly efficient transfection method. Prostate 41:121–126, 1999. © 1999 Wiley-Liss, Inc.
Reliability and Security Monitoring of Virtual Machines Using Hardware Architectural Invariants (2014)

This paper presents a solution that simultaneously addresses both reliability and security (RnS) in a monitoring framework. We identify the commonalities between reliability and security to guide the design of Hyper Tap, a hyper visor-level framework that efficiently supports both types of monitoring in virtualization environments. In Hyper Tap, the logging of system events and states is common across monitors and constitutes the core of the framework. The audit phase of each monitor is implemented and operated independently. In addition, Hyper Tap relies on hardware invariants to provide a strongly isolated root of trust. Hyper Tap uses active monitoring, which can be adapted to enforce a wide spectrum of RnS policies. We validate Hyper Tap by introducing three example monitors: Guest OS Hang Detection (GOSHD), Hidden Root Kit Detection (HRKD), and Privilege Escalation Detection (PED). Our experiments with fault injection and real root kits/exploits demonstrate that Hyper Tap provides robust monitoring with low performance overhead.
Concentration-Dependent Activity of Hydromethylthionine on Cognitive Decline and Brain Atrophy in Mild to Moderate Alzheimer’s Disease (2019)

Hydromethylthionine has pharmacological activity on brain structure and function at the 8 mg/day dose as monotherapy or as add-on to symptomatic treatments. This combined with a plateau at higher doses is consistent with the lack of dose-response seen in the Phase III trials. Treatment benefit is predicted to be maximal at 16 mg/day as monotherapy. A placebo-controlled trial in mild/moderate AD is now ongoing to confirm efficacy at this dose.
Nanosuspensions: a promising drug delivery strategy (2004)

Nanosuspensions have emerged as a promising strategy for the efficient delivery of hydrophobic drugs because of their versatile features and unique advantages. Techniques such as media milling and high-pressure homogenization have been used commercially for producing nanosuspensions. Recently, the engineering of nanosuspensions employing emulsions and microemulsions as templates has been addressed in the literature. The unique features of nanosuspensions have enabled their use in various dosage forms, including specialized delivery systems such as mucoadhesive hydrogels. Rapid strides have been made in the delivery of nanosuspensions by parenteral, peroral, ocular and pulmonary routes. Currently, efforts are being directed to extending their applications in site-specific drug delivery.
DETERMINANTS OF PATIENT SATISFACTION WITH OUTCOME AFTER ANTERIOR CRUCIATE LIGAMENT RECONSTRUCTION (2002)

Univariate and multivariate determinants of patient satisfaction with the outcome after reconstruction of the anterior cruciate ligament were established. Although some specific surgical and objective variables were important, subjective variables of symptoms and function had the most robust associations with patient satisfaction. In assessing the outcome of reconstruction from the perspective of patient satisfaction with the outcome, we should emphasize patient-derived subjective assessment of symptoms and function, particularly those involving issues of stiffness, giving-way, swelling, and patellofemoral symptoms.
A Randomized, Double‐Blind, Placebo‐Controlled Trial of Dexamethasone in Severe Respiratory Syncytial Virus (RSV) Infection: Effects on RSV Quantity and Clinical Outcome (2002)

Forty-one previously healthy children <2 years of age who required mechanical ventilation for respiratory syncytial virus (RSV) infection were randomized to receive dexamethasone (0.5 mg/kg; n=22) or saline placebo (n=19) intravenously every 12 h for 4 days. RSV quantity was measured by quantitative plaque assay in fresh tracheal and nasal aspirates obtained at intervals of 24+/-3 h on days 0, 1, 2, 5, and 7 following entry. Analysis by linear mixed-effects modeling demonstrated a significantly greater decline in mean tracheal RSV quantity in the placebo group than in the dexamethasone group from day 0 to day 1 (0.82 vs. 0.21 log pfu/mL; P=.01) and from day 0 to day 2 (1.45 vs. 0.53 log pfu/mL; P=.03). No differences were found between groups in nasal RSV quantity, white blood cell counts in tracheal or nasal aspirates, serum neutralizing antibody titers during convalescence, or duration of mechanical ventilation, intensive care unit stay, or hospital stay.
Avian B-Cell Development: Generation of an Immunoglobulin Repertoire by Gene Conversion (1991)

The vertebrate B-cell repertoire is capable of generating up to 10(9) different antibody molecules using relatively few germline immunoglobulin (Ig) gene segments. To generate diversity, humans and mice depend on combinatorial and junctional variations that occur during the gene rearrangement events that produce complete heavy and light chain Ig genes. This gene rearrangement process goes on continuously in the bone marrow, where each developing B cell assembles a unique heavy and light chain Ig gene from families of functional V, D, and J gene segments. In contrast, chickens have only single functional V and J segments for the heavy and light chain loci, and chicken Ig gene rearrangement occurs only during a brief period of embryonic development. A specialized organ involved in avian B-cell development, the bursa of Fabricius, provides the microenvironment necessary for the amplification of B cells that have undergone productive Ig gene rearrangements. Within the bursa, B cells also acquire somatic diversity within the rearranged V gene segments of the heavy and light chain Ig loci. Somatic diversification of chicken V gene segments occurs by intrachromosomal gene conversion, a DNA recombination process which involves unidirectional transfer of nucleotide sequence blocks from families of V region pseudogenes into the functional rearranged VH and VL genes.
Quantitative Measurement of Optical Parameters in the Breast Using Time-Resolved Spectroscopy Phantom and Preliminary In Vivo Results (1994)

The authors were able to measure the optical parameters quantitatively using time-resolved spectroscopy. This optical information will contribute to the investigation of photon migration in the breast.
ADVANCES IN ELECTRICAL ASSIST DEVICES (1977)

Marked improvements were realized in the development of electrically driven left ventricular assist systems. A volume reduction of 46%, a system weight reduction of 63%, and a factor of 2 improvement in overall efficiency (29%) were realized. The system, operating at a pressure of 120 mm Hg with a flow rate of approximately 7 L, requires only 7.5 W of input power. In addition, a unique brushless commutator was designed to replace standard brushes, thus increasing system life. A new polyurethane was synthesized for utilization in the TMS. This material has demonstrated high flex life in addition to being biocompatible. Further improvements in system weight and size, as well as efficiency, will be realized when flat plate pumps are mated to electric drivers.
Nuisances olfactives en station d'épuration des eaux : méthodologie de caractérisation des émissions (1992)

International audience
Serum Lithium Determinations for Clinical Use (1967)

AbstractSerum lithium determinations are of value for the adjustment of dosage during lithium treatment of manic-depressive psychosis. A study has been made of the chemical and physical variables which may influence the flame photometric lithium determination, and a practical method for serum lithium determinations is described.Key Words: Lithiumpsychosismanic-depressivespectrophotometry
Postoperative rotation of a 3-piece loop-haptic acrylic intraocular lens (2009)

Postoperative rotation of the loop-haptic IOL was stable; LEC clearance did not adversely affect performance. The tendency toward counterclockwise rotation would not preclude good performance of a toric model of the IOL.
Promoter Hypermethylation in Tumour Suppressor Genes Shows Association with Stage, Grade and Invasiveness of Bladder Cancer (2008)

The results suggest analysis of promoter hypermethylation as a valuable biomarker for prognosis of the aggressive course of disease in bladder cancer.
Enhanced anti-tumor activity of dipeptidyl peptidase inhibitor PT-100 in combination with chemotherapy in mice. (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

3820 

The amino boronic dipeptide, Val-boro-Pro (PT-100), competitively inhibits the dipeptidyl peptidase activity of fibroblast activation protein (FAP) and CD26/DPP-IV. We previously observed that PT-100 significantly inhibited growth of established tumors in mouse models, whereas treatment at earlier stages resulted in rejection of tumors derived from fibrosarcoma and lymphoma cell lines. The activity of PT-100 involved rapid up-regulation of cytokines and chemokines in the tumor and draining lymph node tissue followed by a tumor-specific immune response. CD26/DPP-IV was not the essential molecular target because the anti-tumor activity was undiminished in CD26−/− mice. We have found that FAP mRNA was expressed in lymph nodes proximal to solid tumors in mice, and as shown by others, FAP was expressed within in vivo tumors. FAP associated with the tumor stroma is thought to play a role in tissue re-modeling required for tumor growth by digestion of collagen I in extracellular matrix. The increased production of cytokines and chemokines observed in PT-100-treated mice indicates an additional regulatory role for FAP. The mechanism of action suggests that PT-100 is uniquely suited for use in combination with other anti-cancer agents; consequently, we have investigated treatment of established tumors in mice with PT-100 plus various chemotherapeutic agents, including cisplatin, paclitaxel and 5-fluorouracil. The addition of PT-100 was found to enhance the activity of each agent. In this study, the combination of PT-100 with gemcitabine was highly effective, as shown in the [Table][1]. For each dose of gemcitabine, the combination had a significantly ( P ≤ 0.05) greater anti-tumor effect than treatment with either agent alone. Tumors were never rejected in mice treated with PT-100, and rejection frequencies did not exceed 20% with any dose of gemcitabine; however, combination treatment caused rejection in 40–60% of mice by day 25 after tumor inoculation, and relapses were not observed over a further 30 days. Treatment with cisplatin and PT-100 similarly increased rejection frequency from 20% in mice treated with 5 mg/kg cisplatin alone to 50%. Following tumor rejection, mice were specifically immune to rechallenge with WEHI 164 tumor cells. Thus PT-100 could stimulate tumor immunity in mice that received active doses of chemotherapy.



![Figure][2] [1]: #F1
 [2]: pending:yes
Charge Summing in Spectroscopic X-Ray Detectors With High-Z Sensors (2013)

The spectroscopic performance of photon counting detectors is limited by the effects of charge sharing between neighboring pixels and the emission of characteristic X-rays. For these reasons, an event can be either missed or counted more than once. These effects become more and more of a concern when pixel pitches are reduced, and for the technology available so far, this meant that there would always be a trade-off between a high spatial and a high spectral resolution. In this work, we present first measurements obtained with the new Medipix3RX ASIC, which features a network of charge summing circuits establishing a communication between pixels which helps to mitigate these effects. Combined with cadmium telluride sensors, we show that this new technology is successful at improving a detector's spectroscopic capabilities even at pixel pitches as small as 55 μm. At this pitch, we measure an energy response function similar to that observed for a pixel pitch of 165 μm in the absence of a charge summing circuitry. This amounts to an effective reduction of the pixel area by at least one order of magnitude at a comparable energy response. Additionally, we present synchrotron measurements at high X-ray fluxes, where significant pulse pile-up occurs, and provide first experimental evidence for a net benefit when balancing spectroscopic performance and high flux tolerance in charge summing mode.
An ILP Method Based on Instance Graph (2000)

A necessary function of ILP systems is to test whether rulesets intensionally cover examples. In general, when R contains recursive clauses, the above test may not terminate. In order that ILP techniques can serve end users directly in applications such as knowledge discovery in databases, general methods must be provided to ensure that the learned rulesets are executable and, in particular, that they do not lead to infinite recursion. To the best of our knowledge, all current methods are based on some kind of “Literal Order ” or analog. Among them, the method “Ordering a Set of Constants and then Ordering Recursive Literals ” that FOIL used (Cameron-Jones &amp; Quinlan 1993) is one of the most advanced. However, this method suffers in at least three ways. ¶It can not be extended to Multiple Predicate Learning (MPL) (Raedt et cl. 1993) that involves more than one relation, e.g. when relation R invokes S and S invokes R. ·It may not order constants correctly so as to have to rely on users to define constant orders for many recursive learning tasks. Sometimes this is necessary but not easy for users. ¸It needs to define theory constants that are strong hints of ground clauses. In our opinion, in order to overcome the above shortcomings, FOIL should memory more of previous learning to help further search in rule space. If we can efficiently record and update the effects that are made to the instance space every time when a new (recursive) clause is added to the rule, we can design more powerful heuristics to help search the rule space. Based on this idea, we invented instance graph H(R,E), where R is a ruleset and E is an instance space. u vi true Fig. 1 vj1
Investigation of InGaP/GaAs single and double heterojunction bipolar transistors by doping spike (2002)

The InGaP/GaAs single and double heterojunction bipolar transistors (S- and D-HBT) using a doping spike of 2/spl times/10/sup 12/ cm/sup -2/ located at heterointerfaces have been successfully fabricated with inclusion of study of potential barrier. It is found that a doping spike at emitter-base heterointerface could effectively reduce the potential barrier under forward biased condition and increase the process yield while not as to degrade the device performances. The SHBTs exhibit a common-emitter current gain as high as 410 with a very small offset voltage of 55 mV. The fabricated DHBT's have a common-emitter current gain of 360. Further, the collector-emitter saturation (knee) voltage is lower than 2.0 V. Along with wide-gap collector and low knee voltage, the DHBTs are very promise in application to high-power system.
Management of a large mucosal defect after duodenal endoscopic resection (2016)

Duodenal endoscopic resection is the most difficult type of endoscopic treatment in the gastrointestinal tract (GI) and is technically challenging because of anatomical specificities. In addition to these technical difficulties, this procedure is associated with a significantly higher rate of complication than endoscopic treatment in other parts of the GI tract. Postoperative delayed perforation and bleeding are hazardous complications, and emergency surgical intervention is sometimes required. Therefore, it is urgently necessary to establish a management protocol for preventing serious complications. For instance, the prophylactic closure of large mucosal defects after endoscopic resection may reduce the risk of hazardous complications. However, the size of mucosal defects after endoscopic submucosal dissection (ESD) is relatively large compared with the size after endoscopic mucosal resection, making it impossible to achieve complete closure using only conventional clips. The over-the-scope clip and polyglycolic acid sheets with fibrin gel make it possible to close large mucosal defects after duodenal ESD. In addition to the combination of laparoscopic surgery and endoscopic resection, endoscopic full-thickness resection holds therapeutic potential for difficult duodenal lesions and may overcome the disadvantages of endoscopic resection in the near future. This review aims to summarize the complications and closure techniques of large mucosal defects and to highlight some directions for management after duodenal endoscopic treatment.
Negative bias temperature instability in triple gate transistors (2004)

Negative bias temperature instability (NBTI) in triple gate transistors was investigated for the first time. It is found that the threshold voltage shift caused by negative bias temperature stress in conventional configuration of triple gate transistors is worse than that in planar transistors. This is due to the larger trap state density of the [110] side surface of the active silicon and it is verified by comparing two types of triple gate transistors each of which has [110] side surface and (100) side surface. The <100>-direction channel is proposed as one of the structural options to reduce the degradation of NBTI in triple gate transistors.