gebhart/patrepeval huggingface dataset:
An approximate multi-word matching algorithm for robust document retrieval (2006)

Document generation from low level data and its utilization is one of the most challenging tasks in document engineering. Word occurrence detection is a fundamental problem in the recognized document utilization obtained by a recognizer, such as OCR and speech recognition. Given a set of words, such as a dictionary, this paper proposes an efficient dynamic programming (DP) algorithm to find the occurrences of each word in a text. In this paper, the string similarity is measured by a statistical similarity model that enables a definition of the similarities in the character level as well as edit operation level. The proposed algorithm uses tree structures to measure similarities in order to avoid measuring similarities of the same substrings appearing in different parts of the text and words. The time complexity of the proposed algorithm is O(|W|⋅|S|⋅|Q|), where |W| (resp. |S|) denote the number of nodes in the trees representing the word set (resp. the text), and |Q| donotes the number of the states of the model used for string similarity. This paper shows the proposed algorithm is experimentally about six times faster than a naive DP algorithm.
“Clickable” Polyglycolides:  Tunable Synthons for Thermoresponsive, Degradable Polymers (2008)

“Click” chemistry is a powerful method for post-polymerization modification of polymers and other materials. Because of the importance of lactide-based functional polymers in materials and medical applications, we synthesized 3,6-dipropargyl-1,4-dioxane-2,5-dione, an acetylene-functionalized glycolide monomer. Its subsequent polymerization and copolymerization with lactide provided a new polyglycolide homopolymer as well as random and block copolymers that have pendant acetylene groups available for the attachment of chemical functionality using “click” chemistry. A protocol was devised to permit “click” functionalization of polyglycolides with no degradation in molecular weight. As one demonstration of the power of this approach to substituted polyglycolides, we have prepared a family of degradable, thermoresponsive materials that exhibit lower critical solution temperatures (LCST) from room temperature to >60 °C.
Real-time grasp detection using convolutional neural networks (2015)

We present an accurate, real-time approach to robotic grasp detection based on convolutional neural networks. Our network performs single-stage regression to graspable bounding boxes without using standard sliding window or region proposal techniques. The model outperforms state-of-the-art approaches by 14 percentage points and runs at 13 frames per second on a GPU. Our network can simultaneously perform classification so that in a single step it recognizes the object and finds a good grasp rectangle. A modification to this model predicts multiple grasps per object by using a locally constrained prediction mechanism. The locally constrained model performs significantly better, especially on objects that can be grasped in a variety of ways.
Bactericidal Activity of Soymilk Fermentation Broth by In Vitro and Animal Models (2012)

Soybean fermentation broth (SFB) exhibits potent antibacterial activity against different species of bacteria in in vitro assays and animal models. Four isoflavone compounds-daidzin, genistin, genistein, and daidzein-of SFB were analyzed and quantified by high-performance liquid chromatography. In the in vitro test, daidzin and daidzein had more potent antibacterial activity than genistin. The minimum inhibition concentration values for these bacteria of SFB ranged from 1.25% to 5%, and the minimum bactericidal concentration values of strains ranged from 2.5% to 10%, depending on the species or strain. Vancomycin-resistant Entercoccus faecalis (VRE) strains were also tested for susceptibility to SFB in two species of animal model: the Sprague-Dawley rat and the BALB/c mouse. SFB-fed Sprague-Dawley rats showed excellent elimination efficiency against VRE, close to 99% compared with the phosphate-buffered saline-fed control group. In the BALB/c mouse model, SFB antibacterial activity was 65-80% against VRE compared with the control. In conclusion, SFB contains natural antibacterial substances such as daidzin, genistin, and daidzein that inhibit bacterial growth.
Prognostic significance of the expression of vascular endothelial growth factors A, B, C, and D and their receptors R1, R2, and R3 in patients with nonsmall cell lung cancer (2009)

The results of the current study indicated that the over-expression of VEGFs and VEGFRs plays an important role in the survival of patients with NSCLC. The inclusion of angiogenic factors in the standard pathologic study of lung cancer may improve the clinical evaluation of patients with NSCLC.
Purification and properties of NADP-dependent glutamate dehydrogenase from Ruminococcus flavefaciens FD-1 (1992)

Glutamate dehydrogenase (GDH) (L-glutamate:NADP+ oxidoreductase, deaminating, EC 1.4.1.4) from the cellulolytic ruminal bacterium Ruminococcus flavefaciens has been purified and characterized. The native enzyme and subunit are 280 and 48 kDa, respectively, suggesting that the native enzyme is a hexamer. The enzyme requires 0.5 M KCl for optimal activity and has a pH optimum of 6.9 to 7.0. The Kms for ammonia, alpha-ketoglutarate, and glutamate are 19, 0.41, and 62 mM, respectively. The sigmoidal NADPH saturation curve revealed positive cooperativity for the binding of this coenzyme. The first residue in the N-terminal amino acid sequence from R. flavefaciens GDH was alanine, suggesting that the protein may be modified posttranslationally. Comparison of the N-terminal sequence with those of Escherichia coli, Salmonella typhimurium, and Clostridium symbiosum revealed only 39% amino acid homologies. The GDH from R. flavefaciens was unique in that its specific activity was highest during ammonia-limited growth but was not affected by ammonia shock treatment (20 mM).
Centroamérica, la crisis cafetalera : Efectos y estrategias para hacerle frente (2004)

This study is of particular relevance as coffee is the most important agricultural commodity in the world, and approximately 25 million families-many of them small and medium producers-in 51 countries make a living from it. When world market prices cover production costs, coffee has had an important impact on poverty alleviation, raising thousands of families out of poverty for generations. When prices decline, such as during the recent coffee surpluses, the impact worldwide -and in Central America where this study concentrates its analysis- are profound. Although families develop survival strategies, the impact is significant and, in the most recent crisis, many families have had to abandon their farms. The study shows the economic and social effects of the crisis in terms of reduced production, employment and exports, and environmentally when land use is changed. More importantly, given the vital role coffee plays in the rural economy and in poverty reduction, recommendations are made that transcend the region -on how to maintain market share, value and a competitive edge in the future- thereby mitigating or avoiding the negative impact of similar crises in the seemingly inevitable market swings.
Synthesis of Halogenated Phenols by Directed ortho-Lithiation and ipso-Iododesilylation Reactions of O-Aryl N-Isopropylcarbamates (2006)

The regioselective synthesis of halogenated phenols via directed ortho-lithiation reactions of in situ N-silylated O-aryl N-isopropylcarbamates is reported. This protocol is complemented by ipso-iododesilylation reactions of C-silylated carbamates and iodine-magnesium exchange reactions, which are facilitated by the adjacent carbamoyl group. These methods provide an entry into a series of o-fluoro-, o-iodo-, and o,o′-diiodophenols in high yields which are otherwise difficult to obtain.
Multicomponent Synthesis and Biological Evaluation of a Piperazine-Based Dopamine Receptor Ligand Library (2015)

A series of 1,4-disubstituted piperazine-based compounds were designed, synthesized, and evaluated as dopamine D2/D3 receptor ligands. The synthesis relies on the key multicomponent split-Ugi reaction, assessing its great potential in generating chemical diversity around the piperazine core. With the aim of evaluating the effect of such diversity on the dopamine receptor affinity, a small library of compounds was prepared, applying post-Ugi transformations. Ligand stimulated binding assays indicated that some compounds show a significant affinity, with K i values up to 53 nM for the D2 receptor. Molecular docking studies with the D2 and D3 receptor homology models were also performed on selected compounds. They highlighted key interactions at the indole head and at the piperazine moiety, which resulted in good agreement with the known pharmacophore models, thus helping to explain the observed structure-activity relationship data. Molecular insights from this study could enable a rational improvement of the split-Ugi primary scaffold, toward more selective ligands.
Prospective Comparison of Whole-Blood- and Plasma-Based Hepatitis C Virus RNA Detection Systems: Improved Detection Using Whole Blood as the Source of Viral RNA (1999)

We previously demonstrated that whole blood contains significantly more hepatitis C virus (HCV) RNA than plasma. To validate the whole-blood-based HCV RNA detection method, a prospective comparison of HCV RNA detection in whole blood and plasma from 50 patients with chronic liver disease was undertaken. Whole-blood and plasma aliquots were independently tested for HCV RNA by reverse transcriptase (RT) PCR assay, and plasma was tested by the Roche Amplicor assay. HCV RNA was detected in 35 of 50 (70%) whole-blood samples by RT-PCR but in only 26 of 50 (52%) plasma samples tested by the Amplicor assay (P < 0.01). HCV RNA was detected in 85% of HCV antibody-positive patients by the whole-blood method compared with 74% of plasma samples by the Amplicor method. The five HCV antibody-positive subjects who were negative by whole-blood-based RT-PCR assay were all receiving interferon therapy and had normal transaminases at the time of testing. HCV RNA was detected in 38% of HCV antibody-negative subjects by the whole-blood-based RT-PCR assay compared with 6.25% of these patients by the Amplicor assay (P < 0. 05). There were nine samples in which HCV RNA was detected in whole blood but the Amplicor test was negative. Eight of the nine RNAs prepared from these whole-blood samples tested positive in the Amplicor assay, thus confirming the specificity of our results. This study demonstrates that whole-blood-based HCV RNA detection is more sensitive than currently available commercial tests and that whole-blood RNA is suitable for use in commercial assays.
Retrospective Analysis of the Association Between Demodex Infestation and Rosacea (2010)

A significant association exists between Demodex infestation and the development of rosacea. Demodex infestation is a vital risk factor for rosacea according to the time-to-event relationship, and the degree of infestation played a more important role than did the mite infestation rate in the development of rosacea.
Dual-energy computed tomography imaging to determine atherosclerotic plaque composition: A prospective study with tissue validation (2014)

DECT improves the differentiation of necrotic core and fibrous plaque in ex vivo postmortem arteries. However, much of this improvement is lost when translated to in vivo imaging because of a reduction in image quality.
Phase II trial of topically applied miltefosine solution in patients with skin-metastasized breast cancer (1999)

Skin deposits from breast cancer can present serious therapeutic problems, especially when resistant to conventional therapy. Topical application of a cytotoxic drug may represent an attractive new treatment modality devoid of major systemic toxicity. Miltefosine was selected because of its efficacy in breast cancer models. A mixture of alkylated glycerols of various chain lengths and water was used as the pharmaceutical vehicle to dissolve and to further facilitate tissue penetration of miltefosine. In our Institute a phase II study was performed to determine the efficacy and tolerability of topically applied miltefosine in patients with cutaneous metastases from breast cancer. Thirty-three patients in total entered the trial. A 6% miltefosine solution was applied once daily in the first week and twice daily in the following weeks. The planned minimum treatment duration was 8 weeks. We found an overall response rate of 43% for 30 evaluable patients, composed of 23% complete response and 20% partial response. The median response duration was 18 weeks, range 8-68. Toxicity consisted mainly of localized skin reactions, which could be controlled by a paraffin-based skin cream and, where appropriate, by dose modification. No systemic toxicities were observed. We conclude that topical miltefosine is an effective treatment modality in patients with skin metastases from breast cancer.
Waveform substitution techniques for recovering missing speech segments in packet voice communications (2005)

Packet communication systems cannot, in general, guarantee accurate and prompt delivery of every packet. The effect of network congestion and transmission impairments on data packets is extended delay; in voice communications these problems lead to lost packets. This paper describes techniques for replacing missing speech with waveform segments from correctly received packets in order to increase the maximum tolerable missing packet rate. After presenting a simple formula for predicting the probability of waveform substitution failure as a function of packet duration and packet loss rate, we introduce two techniques for selecting substitution waveforms. One method is based on pattern matching and the other technique explicitly estimates voicing and pitch. Both approaches achieve substantial improvements in speech quality relative to silence substitution.
Novel serum protein biomarkers indicative of growth hormone doping in healthy human subjects (2011)

The detection of recombinant human growth hormone (rhGH) is difficult due to its short half-life; therefore, novel and robust biomarkers of rhGH abuse are needed. In this study, serum samples derived from subjects treated with rhGH in a randomized, double blind, placebo-controlled crossover study were analyzed by 2-DE coupled with MS. Eight healthy male subjects aged 23.2±0.6 years were injected with rhGH (2 mg/day) or saline for 7 days with serum samples drawn at days 0, 3, and 8. Protein intensities were quantified and analyzed for differences between rhGH and placebo treatments. Proteins that showed significant changes were identified and confirmed by Western blotting. These included specific isoforms of α-1 antitrypsin and transthyretin that increased; and inter-α-trypsin inhibitor heavy chain H4, apolipoprotein A-1, and hemoglobin β chain that decreased. These proteins represent novel biomarkers of short-term rhGH exposure and may lead to a new method for detecting rhGH doping.
Aβ1–42 inhibition of LTP is mediated by a signaling pathway involving caspase-3, Akt1 and GSK-3β (2011)

Amyloid-β(1-42) (Aβ) is thought to be a major mediator of the cognitive deficits in Alzheimer's disease. The ability of Aβ to inhibit hippocampal long-term potentiation provides a cellular correlate of this action, but the underlying molecular mechanism is only partially understood. We found that a signaling pathway involving caspase-3, Akt1 and glycogen synthase kinase-3β is an important mediator of this effect in rats and mice.
Space-frequency turbo coded OFDM for future high data rate wideband radio systems (2002)

A new bandwidth and power efficient signaling scheme is proposed that achieves high data rates over wideband radio channels exploiting the bandwidth efficient OFDM modulation, multiple transmit and receive antennas and large frequency selectivity offered in typical low mobility indoor environments. Owing to its maximum transmit diversity gain and large coding gain, space-frequency turbo coded modulation is demonstrated to perform within 2.5 dB of the 10% outage capacity for the variety of practical wideband MIMO radio channels, strongly outperforming other space-frequency coding schemes recently proposed in the literature. A simple way of combining space-frequency coding with OFDM delay diversity for cost effective exploitation of more than two transmit antennas is also proposed.
Detecting Respiratory Viruses in Asymptomatic Children (2012)

Molecular assays may have several advantages over conventional methods for detecting respiratory viruses, including improved sensitivity and rapid detection, but given the high prevalence of positive results in children without RVI symptoms, results should be interpreted cautiously.
T-box genes coordinate regional rates of proliferation and regional specification during cardiogenesis (2005)

Mutations in T-box genes are the cause of several congenital diseases and are implicated in cancer. Tbx20-null mice exhibit severely hypoplastic hearts and express Tbx2, which is normally restricted to outflow tract and atrioventricular canal, throughout the heart. Tbx20 mutant hearts closely resemble those seen in mice overexpressing Tbx2 in myocardium, suggesting that upregulation of Tbx2 can largely account for the cardiac phenotype in Tbx20-null mice. We provide evidence that Tbx2 is a direct target for repression by Tbx20 in developing heart. We have also found that Tbx2 directly binds to the Nmyc1 promoter in developing heart, and can repress expression of the Nmyc1 promoter in transient transfection studies. Repression of Nmyc1 (N-myc) by aberrantly regulated Tbx2 can account in part for the observed cardiac hypoplasia in Tbx20 mutants. Nmyc1 is required for growth and development of multiple organs, including the heart, and overexpression of Nmyc1 is associated with childhood tumors. Despite its clinical relevance, the factors that regulate Nmyc1 expression during development are unknown. Our data present a paradigm by which T-box proteins regulate regional differences in Nmyc1 expression and proliferation to effect organ morphogenesis. We present a model whereby Tbx2 directly represses Nmyc1 in outflow tract and atrioventricular canal of the developing heart, resulting in relatively low proliferation. In chamber myocardium, Tbx20 represses Tbx2, preventing repression of Nmyc1 and resulting in relatively high proliferation. In addition to its role in regulating regional proliferation, we have found that Tbx20 regulates expression of a number of genes that specify regional identity within the heart, thereby coordinating these two important aspects of organ development.
Validation for Clinical Use of, and Initial Clinical Experience with, a Novel Approach to Population-Based Carrier Screening using High-Throughput, Next-Generation DNA Sequencing (2014)

Traditional carrier screening assays are designed to look for only the most common mutations within a gene owing to cost considerations. Although this can yield high detection rates in specific populations for specific genes (such as cystic fibrosis in Caucasians), they are suboptimal for other ethnicities or for patients of mixed or unknown ethnic background. Next-generation DNA sequencing provides an opportunity to provide carrier screening using more comprehensive mutation panels that are limited primarily by information about the clinical impact of detected sequence changes. We describe a next-generation DNA sequencing-based assay capable of reliably screening patient samples in a timely and comprehensive manner. The analytic accuracy in a research setting has been documented. Here, we describe the additional studies performed to ensure the accuracy (analytic validity) and robustness of our assay for use in clinical practice and provide data from our experience offering this testing. Our clinical experience using this approach to screen 11,691 in vitro fertilization patients has identified 449 mutant alleles: 447 in carriers and 2 in an affected individual. In total, we found 87 distinct mutations in 14 different genes. Approximately one quarter of the mutations found are not included in traditional, limited, mutation panels, including 16 known mutations unique to our panel, and novel truncating mutations in several genes.
Computing Polynomials with Positive Coefficients using Stochastic Logic by Double-NAND Expansion (2017)

This paper proposes a novel method, referred to as \textit{double-NAND expansion}, to implement polynomials with all positive coefficients using unipolar stochastic logic. %The inputs and outputs of these circuits lie between 0 and 1, and are encoded using unary bit streams. Prior work has addressed implementation of polynomials with alternately positive and negative coefficients and non-increasing magnitudes, using stochastic logic based on Horner's rule. However, Horner's expansion is not applicable to implementation of polynomials with all positive coefficients. The proposed double-NAND expansion leads to implementations of polynomials using no more than 2n NAND gates where n represents the degree of the polynomial. %While the Horner's rule leads to cascaded AND-NAND gates, the proposed expansion leads to cascaded double-NAND gates.The proposed implementations are compared with those based on multiplexers, Bernstein polynomial method, finite state machine method and factorization. The paper also considers implementations of several functions expressed as polynomials using truncated Mclaurin series based on the proposed approach. The experimental results show that the proposed method outperforms the prior methods in terms of accuracy, hardware complexity, and critical path.
Regulation of presynaptic phosphatidylinositol 4,5-biphosphate by neuronal activity (2001)

Phosphatidylinositol 4,5-biphosphate (PIP2) has been implicated in a variety of cellular processes, including synaptic vesicle recycling. However, little is known about the spatial distribution of this phospholipid in neurons and its dynamics. In this study, we have focused on these questions by transiently expressing the phospholipase C (PLC)-delta1 pleckstrin homology (PH) domain fused to green fluorescent protein (GFP) in cultured hippocampal neurons. This PH domain binds specifically and with high affinity to PIP2. Live confocal imaging revealed that in resting cells, PH-GFP is localized predominantly on the plasma membrane. Interestingly, no association of PH-GFP with synaptic vesicles in quiescent neurons was observed, indicating the absence of detectable PIP2 on mature synaptic vesicles. Electrical stimulation of hippocampal neurons resulted in a decrease of the PH-GFP signal at the plasma membrane, most probably due to a PLC-mediated hydrolysis of PIP2. This was accompanied in the majority of presynaptic terminals by a marked increase in the cytoplasmic PH-GFP signal, localized most probably on freshly endocytosed membranes. Further investigation revealed that the increase in PH-GFP signal was dependent on the activation of N-methyl-D-aspartate receptors and the consequent production of nitric oxide (NO). Thus, PIP2 in the presynaptic terminal appears to be regulated by postsynaptic activity via a retrograde action of NO.