gebhart/patrepeval huggingface dataset:
Accurate typing of HLA‐A antigens and analysis of serological deficiencies (1997)

We are reporting the results of HLA-A typing by PCR-SSOP complemented by PCR-SSP of samples obtained from the National Marrow Donor Program (NMDP). These samples were a representative group from 2486 tested in duplicate by serology. A total of 390 samples gave HLA-A discrepant results. Comparing the molecular typing results of 238 samples (samples with available DNA) with the serological typing results, 54 homozygotes and 184 heterozygotes produced a total of 422 assignments by molecular methods. We found assignment discrepancies in 147/422 (35%) in laboratory 1 and 144/422 (34%) in laboratory 2 (a combined group of 4 NMDP laboratories; laboratory 1 is not included). The serological discrepancies found were of 3 categories: a) false negatives, b) incomplete typing (discrepancies due to the level of resolution within a cross-reactive or CREG group) and c) false positives. Major problems were identified using serology for typing HLA-A antigens: a) inability to identify all WHO-recognized specificities, more frequently in non-Caucasians or in HLA-A specificities known to be found more frequently in non-Caucasians for laboratory 1 and incorrect assignments of A19 specificities in laboratory 2, b) incorrect assignments in cells with poor viability and c) false-positive assignments in homozygotes. We propose a possible strategy to type HLA-A specificities with two steps: a) a minimum of serology for typing specificities for common CREG groups: A1, A2, A3, A11, A9, A10, A28, A19. However, a given laboratory can determine the level of serological assignments needed as a first step. And b) molecular methods to identify splits: A23, A24, A29, A30, A31, A32, A33, A34, A36, A66, A74 and A80. The technique described is useful for large-scale bone marrow donor typings for cells with poor viability, and for resolving ambiguous results including false-positive assignments of homozygous cells.
Emergence of azole resistant-Aspergillus fumigatus infections during STAT3-deficiency (2020)

<b>Introduction.</b> Signal transducer and activator of transcription 3 (STAT3) deficiency is a rare primary immunodeficiency associated with increased susceptibility to bacterial and fungal infections, notably pulmonary aspergillosis.<b>Aim.</b> We describe the emergence of azole-resistant <i>Aspergillus fumigatus</i> infections in STAT3-deficient patients.<b>Methodology.</b> During a retrospective study of 13 pulmonary aspergillosis cases in STAT3-deficient patients conducted in France, we identified patients infected with azole-resistant <i>A. fumigatus</i> isolates.<b>Results.</b> Two out of the 13 STAT3-deficient patients with aspergillosis had azole-resistant <i>A. fumigatus</i> infection, indicating an unexpectedly high prevalence of resistance. The first patient with STAT3 deficiency presented several flares of allergic bronchopulmonary aspergillosis-like episodes. He was chronically infected with two azole-resistant <i>A. fumigatus</i> isolates (TR<sub>34</sub>/L98). Despite prolonged antifungal treatment, including caspofungin and amphotericin B, the patient was not able to clear the azole-resistant <i>A. fumigatus</i>. The second patient had chronic cavitary pulmonary aspergillosis (CCPA). The <i>A. fumigatus</i> isolate was initially azole susceptible but harboured three F46Y, M172V and E427K point mutations. Despite prolonged antifungal therapies, lesions worsened and the isolate became resistant to all azoles. Surgery and caspofungin treatments were then required to cure CCPA. Resistance was probably acquired from the environment (TR<sub>34</sub>/L98) in the first case whereas resistance developed under antifungal treatments in the second case. These infections required long-term antifungal treatments and surgery.<b>Conclusions.</b> The emergence of azole-resistant <i>A. fumigatus</i> infections in STAT3-deficiency dramatically impacts both curative and prophylactic antifungal strategies. Physicians following patients with primary immune-deficiencies should be aware of this emerging problem as it complicates management of the patient.
Who Knows? Humanities Research in 'Computerized Societies' (2015)

Is it certain that to the word communication corresponds a concept that is unique, univocal, rigorously controllable, and transmittable: in a word, communicable?(Derrida, Limited Inc, 1) Despite the apparent focus on the status of 'knowledge in computerized societies' in his most well-known book (The Postmodern Condition, 3-9), Jean-Franois Lyotard's ideas have generally been taken up less as contributions to media, communication and information studies than as works of philosophy or cultural theory.This is unsurprising perhaps, given that even those of his works that appear to have an explicit focus on communication and information technologies revolve more around ethics (Differend), art and aesthetics (Inhuman), truth and legitimation (Postmodern), than around what we today call (rightly or wrongly) 'new media'.It's interesting to note nevertheless the near prescience of the first few, scene-setting sections to Lyotard's famous 'report on knowledge', in which he forecasts the impact that technological transformations can be expected to have on knowledge.Outside the effects that 'the proliferation of information-processing machines' will have 'on the circulation of learning' (Postmodern, 4), Lyotard highlights the 'exteriorization of knowledge with respect to the "knower"' which exacerbates a process whereby knowledge is commodified for sale, consumption, and subsequent valorization 'in a new production' (ibid.).Read today, in a world where a 'culture of search' defines knowledge acquisition and information exchange, if not many other aspects of life (see Hillis et al., Google), and where academic journal publishing is seriously big business (see Miller, 'Humanities'), Lyotard's predictions look to have paid out.Further, his hypothesis that nation-states-and even 'multinational corporations'-will 'one day fight for control of information, just as they battled in the past for control over territory, raw materials and cheap labor' (Postmodern, 5), seems credible in the wake of WikiLeaks and the Snowden release of US National Security Agency documents, not to mention the reciprocal allegations of cyberwarfare made by the Chinese and US governments.It feels safe to say, then, that Lyotard's analysis makes plain how the age of computerisation raises to the next order of magnitude the question of media power in capitalist culture (see Gane, 'Computerized').By the same token, the critical (and not entirely unexpected) point concerning the political-economy of knowledge production and ownership, couched in terms of control and access, is ghosted in Lyotard's report by a quasi-Romantic disquietude over the reduction of hard-earned knowledge to consumable information.For at the base of these political-economic intensifications lies a more fundamental transformation of the nature of knowledge-its translation into 'quantities of information' so as to enable it to fit into new information-processing channels and new operational imperatives:
Blind Recognition of LDPC Codes Over Candidate Set (2019)

Adaptive modulation and coding (AMC) techniques have attracted more attention recently because of flexible strategies and dynamic channel quality. Blind recognition of encoder is an important technology for AMC systems because it can improve communication efficiency very well. In this letter, we present a new algorithm to tackle blind low-density parity-check (LDPC) encoder identification over a given candidate set. Our proposed scheme establishes a cosine conformity (CC) of syndrome, which is a posterior probability that can measure the probability that all parity check relations of the codes are satisfied, and classifies the LDPC encoder leading to maximum average CC over the candidate set. Simulations show that the new method is effective for LDPC encoder identification; the theoretical correct ratio of recognition is consistent with the simulation results, and its performance is improved by nearly 1.5 dB when compared with the existing algorithm.
Flower-like nanoarchitecture assembled from Bi2S3 nanorod/MoS2 nanosheet heterostructures for high-performance supercapacitor electrodes A Physicochemical and engineering aspects (2017)

Three-dimensional (3D) flower-like Bi2S3/MoS2 nanohybrid is synthesized using a facile one-pot hydrothermal method. In the nanohybrid, MoS2 nanosheet is tightly attached to the surface of the Bi2S3 nanorod to form a superior heterointerface, facilitating the electron transfer. Three-dimensional nanoarchitecture gives rise to large spaces and voids, fastening the ion diffuse. With the unique structural features of high-quality heterostructures and 3D aisles, the as-prepared flower-like Bi2S3/MoS2 nanohybrid exhibit excellent electrochemical performance with a high specific capacitance of 3040Fg⁻¹, a remarkable rate capability (1258Fg⁻¹ at a current density of 30Ag⁻¹), and an outstanding cycle stability (92.65% capacitance retention after 5000 cycles at 10Ag⁻¹). These promising results bring a new strategy to design advanced electrode materials for high-performance supercapacitors.
Hydroxamic Acid Derivatives as Potent Peptide Deformylase Inhibitors and Antibacterial Agents (2000)

Low-molecular-weight beta-sulfonyl- and beta-sulfinylhydroxamic acid derivatives have been synthesized and found to be potent inhibitors of Escherichia coli peptide deformylase (PDF). Most of the compounds synthesized and tested displayed antibacterial activities that cover several pathogens found in respiratory tract infections, including Chlamydia pneumoniae, Mycoplasma pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. The potential of these compounds as antibacterial agents is discussed with respect to selectivity, intracellular concentrations in bacteria, and potential for resistance development.
Evolutionary Actor-Multi-Critic Model for VNF-FG Embedding (2020)

The placement of Virtual Network Function - Forwarding Graphs (VNF-FGs) is one of the basic operations in the networks of the future. Being NP-hard, several heuristics and metaheuristics have been proposed. However, these approaches are inefficient due to the need to recalculate the solution at each service placement. In this paper, we adapt one of the most advanced approaches in Deep Reinforcement Learning (DRL), in order to improve exploration by generalizing the neural network calculating action values. We also propose an evolutionary algorithm to evolve these neural networks in order to discover better ones, which also avoids getting stuck in local minima. In order to avoid going through the almost innumerable number of infeasible solutions, we propose a heuristic, which combined with our DRL, makes it possible to guarantee the feasibility of the solutions and therefore to make the placement much more efficient. The simulation results we obtained confirm the quality of the solutions obtained as well as the superiority of the proposed solution over the existing one.
Beyond the blot: cutting edge tools for genomics, proteomics and metabolomics analyses and previous successes (2012)

The skin has an amazing array of complex interacting biological processes. Recent advances in investigational techniques now allow evaluation of these processes at the level of the gene, protein and metabolite. Sometimes collectively known as the omics, these fields of inquiry, known as genomics, proteomics and metabolomics, respectively, are yielding new and important insights into skin structure and processes, its responses to injury and age, and the mechanisms by which new interventions and compounds may work to improve the health and integrity of this crucial organ.
Small size class AB amplifier for energy harvesting with ultra low power, high gain, and high CMRR (2016)

A low cost, high gain, and ultra low power rail-to-rail input-output amplifier based in 0.18 micron CMOS is presented, whose size is ∼ 77 um per side. This work's incremental contributions are: First, a small and simple regulated cascode current mirror (RGC) is presented that is composed of a common source amplifier coupled with a diode connected self-cascode (SC). This RGC is incorporated in a standard folded cascode amplifier to boost its gain and modestly increase its high impedance output's operating head room, which is beneficial in the sub 1V power supply (VDD) environments. Second, amplifier's inputs can span to the rails via using two pairs of differential PMOSFETs in parallel, where the secondary pair is DC level shifted by NMOSFETs. As the amplifier's inputs span the rails, a single FET steers the same tail current between the amplifier's primary and secondary input PMOSFET pairs, thereby keeping its transconductance almost constant, considering that the amplifier operates in subthreshold. Montecarlo (MC) and worst case (WC) simulations indicate the following specifications are achievable: V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</inf> minimum ∼ 0.8v; I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</inf> ∼ 260nA; input range rail to rail; offset voltage ∼ 5mV; output range ∼ 25mV from the rails; open loop gain (Av) ∼ 138dB with unity gain bandwidth (fu) ∼ 2MHz and phase margin (PM) ∼ 30 degrees; power supply rejection ratio (PSRR) ∼ −120dB; common mode rejection ratio (CMRR) ∼ −140dB; slew rate (SR) ∼ 1V/ uS; settling time (ts) ∼ 3uS.
Experience in Aligning AnatomicalOntologies (2007)

An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning across ontologies. The objective of this paper is to recapitulate our experience in aligning large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus. Their underlying representation formalisms are all different. Our approach to aligning concepts (directly) is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). In addition to point-to-point mapping of concepts, we present the alignment of relationships and the mapping of concepts group-to-group. We have also successfully tested an indirect alignment through a domain-specific reference ontology. We present an evaluation of our techniques, both against a gold standard established manually and against a generic schema matching system. The advantages and limitations of our approach are analyzed and discussed throughout the paper.
Estimation of band level resolutions of human chromosome images (2012)

Current estimation methods for band level resolutions of human chromosome images in cytogenetic laboratories are time consuming and required experienced specialists to manually perform. To alleviate this problem, in this paper, a computerized approach to estimate band level resolution is proposed. The intensity gradient profile and sign profile of chromosome images are utilized to count the number of bands. Then band level resolutions of chromosome images are classified into three categories: 400-, 500-, and 550-band levels by using k-nearest neighbor algorithm. The experimental results show the accuracy of the proposed algorithm. We also provide a discussion on how to improve the overall accuracy.
Radiation Therapy for Patients with Bone Metastasis from Uterine Cervical Cancer: Its Role and Optimal Radiation Regimen for Palliative Care (2018)

Radiation therapy is effective for relief of pelvic symptoms in patients with bone metastasis from uterine cervical cancer. For patients who are expected to survive for more than 1 year, almost curative-dose irradiation to primary tumors is recommended.
Adaptive Doses of MNNG Efficiently Induce a recA-trp Gene Fusion (1983)

The recA gene product plays a critical role in the Escherichia coli SOS system. To facilitate studies of the regulation of the recA operon, we constructed a gene fusion between the recA operon and the Salmonella trp operon. This gene fusion closely mimics the behavior of the authentic recA operon in vivo. Using the gene fusion, we looked at the effect of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) on recA expression. In contrast to the expectations from previous work, we found that low (0.5 microgram/ml) adaptive doses of MNNG induce the recA-trp gene fusion as efficiently as other SOS inducers without inducing either lambda or phi 80 prophages. These results are a clear example of the ability of some agents to induce a subset of the SOS-dependent operons. They force a reevaluation of many of the arguments that have led to the conclusion that the SOS and adaptive responses are completely independent.
Towards a Privacy-Enhanced Social Networking Site (2010)

Social Networking Sites (SNS), such as Facebook and LinkedIn, have become the established place for keeping contact with old friends and meeting new acquaintances. As a result, a user leaves a big trail of personal information about him and his friends on the SNS, sometimes even without being aware of it. This information can lead to privacy drifts such as damaging his reputation and credibility, security risks (for instance identity theft) and profiling risks. In this paper, we first highlight some privacy issues raised by the growing development of SNS and identify clearly three privacy risks. While it may seem a priori that privacy and SNS are two antagonist concepts, we also identified some privacy criteria that SNS could fulfill in order to be more respectful of the privacy of their users. Finally, we introduce the concept of a Privacy-enhanced Social Networking Site (PSNS) and we describe Privacy Watch, our first implementation of a PSNS.
A variable step-size gradient adaptive lattice algorithm for multiple sinusoidal interference cancelation (2013)

Abstract In passive sonar, adaptive algorithms can be used to cancel strong sinusoidal self-interferences. In order to correctly recover low-power target signals during the early stages of processing, these adaptive algorithms must provide fast convergence and, at the same time, narrow notches at the frequencies of the sinusoids. In this respect, the gradient adaptive lattice (GAL) algorithm is a very attractive choice. However, the GAL algorithm with a constant step-size parameter has to compromise between the convergence rate and notch bandwidths. Therefore, in this article, we propose a variable step-size scheme for the GAL algorithm that can achieve both a fast convergence rate and narrow notches. Simulation results demonstrate the efficiency of the proposed algorithm compared to both the conventional GAL algorithm and transversal adaptive filter combined with the variable step-size scheme.
Cardiovascular Disease Risk Factors in Women With a History of Early-onset Preeclampsia (2014)

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THE FORESTRY RECLAMATION APPROACH AND THE MEASURE OF ITS SUCCESS IN APPALACHIA (2009)

The Appalachian Regional Reforestation Initiative (ARRI) is a broad- based citizen/industry/government program working to encourage the planting of productive trees on abandoned and active coal mine lands. Forestry research has confirmed that highly productive forestland can be created on reclaimed mine land by using a five step straight-forward methodology called the Forestry Reclamation Approach (FRA). Data taken from Office of Surface Mining and state regulatory permit and bond release documents indicate that since the start of ARRI in 2005, a gradual increase in the planting of trees on coal surface mines has occurred. ARRI states reported about 9.4 million trees planted in 2005, 11.1 million trees planted in 2006, and 12.8 million trees planted in 2007. However, despite an aggressive technical outreach by ARRI, serious cultural barriers and other impediments to proper surface mine reforestation remain pervasive in the Appalachian coalfields. In 2007, the ARRI states reported that of the 12.8 million trees planted, only 3.4 million trees were planted using the full 5 steps of the FRA. The number of trees planted on conventionally reclaimed sites which were not FRA compliant was estimated at 9.4 million. One or more of the 5 steps of the FRA where not utilized on over two-thirds of the trees planted on surface mines in Appalachia over the past three years.
NewN-Glycans in Horseradish Peroxidase (1998)

We describe here the structures of several new N-glycan oligosaccharides from horseradish peroxidase (HRP). Glycopeptides from HRP were digested with glycoamidase A (from sweet almond) to release the N-glycans. The oligosaccharides were reductively aminated with 2-aminopyridine, and separated by high-performance liquid chromatography on octadecylsilyl- and amide-silica columns for two-dimensional mapping (Tomiya et al., Anal. Biochem. 171, 73-90, 1988). The N-glycans were also analyzed by electrospray ionization mass spectrometry. Two different lots of HRP showed a considerable difference in their N-glycan composition.
A New Target for Therapy in Squamous Cell Carcinoma of the Lung (2011)

Investigators report the identification of novel somatic mutations in the DDR2 kinase gene in squamous cell carcinoma of the lung. Cellular, biochemical, and human data suggest that tumor cells harboring DDR2 mutations have increased sensitivity to existing tyrosine kinase inhibitors, providing rationale for clinical trials of agents that inhibit DDR2 kinase in the disease.