gebhart/patrepeval huggingface dataset:
Recombination rates of genes expressed in human tissues (2007)

High-resolution recombination rates have recently been revealed in the human genome, and considerable variation in patterns of recombination rates has been found along the chromosomes. Although the associations between this variation and genomic sequence features, such as genic regions, provide information on haplotype diversity and natural selection in these regions, the associations are not well understood. Here, we performed microarray experiments to identify genes specifically expressed in human tissues and investigated tendencies of recombination rates within tissue-specific genes. We found that some types of tissue-specific genes (in the frontal lobe, fetal brain, testis, thymus and thyroid) tended to have extremely low recombination rates, whereas other types (in the brain cerebellum, brain whole, stomach, lung and bone marrow) tended to have relatively high recombination rates. Surprisingly, genes specifically expressed in the frontal lobe, which is a brain region involved in human cognitive abilities, had low recombination rates, whereas genes specifically expressed in the cerebellum, which is a brain region with primitive functions shared by all vertebrate species, had high rates. These findings suggest that natural selection forms the recombination rate tendencies according to the physiological functions exerted in the tissues. For example, the low recombination rates in frontal lobe-specific genes may indicate that a few haplotypes have been rapidly widespread across the population because higher cognitive abilities are advantageous. Frontal lobe-specific genes with extremely low recombination rates may be candidates for genes related to cognitive abilities that human species have recently obtained.
Biomimetic Synthesis of the Tumor‐Associated (2,3)‐Sialyl‐T Antigen and Its Incorporation into Glycopeptide Antigens from the Mucins MUC1 and MUC4 (2004)

Glycoproteins on epithelial tumor cells often exhibit aberrant glycosylation profiles. The incomplete formation of the glycan side chains resulting from a down-regulated glucosamine transfer and a premature sialylation results in additional peptide epitopes, which become accessible to the immune system in mucin-type glycoproteins. These cancer-specific structure alterations are considered to be a promising basis for selective immunological attack on tumor cells. Among the tumor-associated saccharide antigens, the (2,3)-sialyl-T antigen has been identified as the most abundant glycan, found in several different carcinoma cell lines. According to a linear biomimetic strategy, the (2,3)-sialyl-T antigen was synthesized by a stepwise glycan chain extension of a protected galactosamine-threonine precursor. For the construction of immunostimulating antigens combining both peptide and saccharide motifs, this antigen was incorporated into glycopeptide partial structures from the mucins MUC1 and MUC4 by sequential solid-phase synthesis.
Transfer Learning with Radio Frequency Signals (2021)

Transfer learning has allowed for more widespread adaptation and expanded use of deep learning models in fields such as computer vision and speech recognition. The radio frequency (RF) domain has lagged behind and has yet to experience similar gains. Yet, at the same time, transfer learning is more relevant to tasks the RF domain. Few large labeled RF datasets exist and when they are available there is typically a difference between the dataset, i.e., the source data, and any target data application due to the myriad of variances that are introduced to RF signals, systems, and environments. Transfer learning focuses directly on this disparity between source and target data and changes in task, making it an ideal candidate to enable more widespread adaptation of deep learning within the RF domain. In this paper we explore several applications of transfer learning to RF signals using both synthetic and real-world communications signals. We focus on an RF fingerprinting task, using our RiftNet model as the base of our deep learning models. This paper presents approaches and results for RF transfer learning in the context of pre-trained models, re-tuning, unsupervised feature learning, and novel device detection. Moving beyond the methods and results presented in this paper, we hope this work motivates others to explore the potential and benefits of RF applications of transfer learning.
Time-domain algorithms for harmonic bandwidth reduction and time scaling of speech signals (1979)

Frequency scaling of speech signals by methods based on short-time Fourier analysis (STFA), analytic rooting, and harmonic compression using a bank of filters, is a complex operation which requires a large amount of computation in a digital implementation. It is shown in this paper that, by incorporating pitch frequency information into a frequency-scaling process based on STFA, it is possible, to a good approximation, to perform this operation in the time domain with very few arithmetic operations (one multiplication and two additions per output sample, in most applications). The derivation of the time-domain harmonic scaling (TDHS) algorithms, selection of parameters, and, in particular, the determination of an appropriate weighting function used in the algorithms, as well as several potential applications, are detailed in the paper. Two proposed applications are discussed in greater detail. These are 1) a vocoder system which incorporates waveform coding of the frequency divided signal (by a factor of up to 3), and 2) a computer-based isolated-word recognition system in which all input utterances are compressed to the same duration at the preprocessing phase effecting an overall computation reduction by a factor of up to 3. Computer simulation results which demonstrate the TDHS algorithms' performance are included.
Effect of inactivation of nuo and ackApta on redistribution of metabolic fluxes in Escherichia coli (1999)

The nuoA-N gene cluster encodes a transmembrane NADH:ubiquinone oxidoreductase (NDH-I) responsible for coupling redox chemistry to proton-motive force generation. Interactions between nuo and the acetate-producing pathway encoded by ackA-pta were investigated by examining the metabolic patterns of several mutant strains under anaerobic growth conditions. In an ackA-pta strain, the flux to acetate was decreased dramatically, whereas flux to lactate was increased significantly when compared with its parent strain; the fluxes to pyruvate and ethanol also increased slightly. In addition, pyruvate was excreted. A strain carrying the nuo mutation showed metabolic flux distribution similar to the wild type. The ackA-pta-nuo strain showed a different metabolic pattern. It not only exhibited reduced acetate accumulation but also significantly lower ethanol and formate synthesis. Metabolic flux distribution analysis suggests that the excessive carbon flux was redirected at the pyruvate node through the lactate dehydrogenase pathway for lactate formation rather than the pyruvate formate-lyase (PFL) pathway for acetyl-CoA and formate production. The diminished capacity through the formate and ethanol (ADH) pathways was not the result of genetic disruption of functional PFL or ADH production. The introduction of a Bacillus subtilis acetolactate synthase gene returned formate, ethanol, and lactate levels to those of the wild type (ackA+pta+nuo+) strain. Furthermore, transfer of a lactate dehydrogenase mutation yielded a strain producing ethanol as the sole fermentation product. As confirmation of the nuo effect, cultures of the ackA-pta strain, supplemented with an NDH-I inhibitor, produced intermediary levels of flux to ethanol and formate. Mutations in both ackA-pta and nuo are required to significantly reduce the flux through the PFL pathway. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 65: 291–297, 1999.
Gene Expression Profiling of Lymphoid Malignancies (2002)

Comprehensive gene expression profiling using DNA microarrays is providing a molecular classification of cancer into disease categories that are homogeneous with respect to pathogenesis and clinical behavior. Gene expression profiling revealed that diffuse large B cell lymphoma (DLBCL) consists of at least two molecularly distinct diseases that are derived from distinct stages of B cell differentiation and have strikingly different clinical outcomes. By contrast, chronic lymphocytic leukemia (CLL) was found to be a single disease defined by a characteristic gene expression signature. Nonetheless, gene expression profiling distinguished two clinically divergent CLL subtypes and provided evidence that signaling through the B cell antigen receptor may play a role in the clinically aggressive subtype. Gene expression analysis also illuminated the mechanism of lymphomagenesis caused by BCL-6 translocations and provided evidence that the NF-kappa B signaling pathway is a new molecular therapeutic target in DLBCL.
Heart Failure and Sudden Death in Patients With Tachycardia-Induced Cardiomyopathy and Recurrent Tachycardia (2004)

Tachycardia-induced cardiomyopathy develops slowly and appears reversible by left ventricular ejection fraction improvement, but recurrent tachycardia causes rapid decline in left ventricular function and development of heart failure. Sudden death is possible.
Phototherapy of Acne Vulgaris with Visible Light (1997)

Visible light is a moderately effective alternative for treatment of acne vulgaris.
Clinical and Laboratory Diagnosis of Dengue Virus Infection (2017)

Infection with any of the 4 dengue virus serotypes results in a diverse range of symptoms, from mild undifferentiated fever to life-threatening hemorrhagic fever and shock. Given that dengue virus infection elicits such a broad range of clinical symptoms, early and accurate laboratory diagnosis is essential for appropriate patient management. Virus detection and serological conversion have been the main targets of diagnostic assessment for many years, however cross-reactivity of antibody responses among the flaviviruses has been a confounding issue in providing a differential diagnosis. Furthermore, there is no single, definitive diagnostic biomarker that is present across the entire period of patient presentation, particularly in those experiencing a secondary dengue infection. Nevertheless, the development and commercialization of point-of-care combination tests capable of detecting markers of infection present during different stages of infection (viral nonstructural protein 1 and immunoglobulin M) has greatly simplified laboratory-based dengue diagnosis. Despite these advances, significant challenges remain in the clinical management of dengue-infected patients, especially in the absence of reliable biomarkers that provide an effective prognostic indicator of severe disease progression. This review briefly summarizes some of the complexities and issues surrounding clinical dengue diagnosis and the laboratory diagnostic options currently available.
MicroRNA-21 Knockdown Disrupts Glioma Growth In vivo and Displays Synergistic Cytotoxicity with Neural Precursor Cell–Delivered S-TRAIL in Human Gliomas (2007)

Despite the development of new glioma therapies that allow for tumor-targeted in situ delivery of cytotoxic drugs, tumor resistance to apoptosis remains a key impediment to effective treatment. Mounting evidence indicates that microRNAs (miRNA) might play a fundamental role in tumorigenesis, controlling cell proliferation and apoptosis. In gliomas, microRNA-21 (miR-21) levels have been reported to be elevated and their knockdown is associated with increased apoptotic activity. We hypothesized that suppression of miR-21 might sensitize gliomas for cytotoxic tumor therapy. With the use of locked nucleic acid (LNA)-antimiR-21 oligonucleotides, bimodal imaging vectors, and neural precursor cells (NPC) expressing a secretable variant of the cytotoxic agent tumor necrosis factor-related apoptosis inducing ligand (S-TRAIL), we show that the combined suppression of miR-21 and NPC-S-TRAIL leads to a synergistic increase in caspase activity and significantly decreased cell viability in human glioma cells in vitro. This phenomenon persists in vivo, as we observed complete eradication of LNA-antimiR-21-treated gliomas subjected to the presence of NPC-S-TRAIL in the murine brain. Our results reveal the efficacy of miR-21 antagonism in murine glioma models and implicate miR-21 as a target for therapeutic intervention. Furthermore, our findings provide the basis for developing combination therapies using miRNA modulation and cytotoxic tumor therapies.
A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis (2009)

This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.
Effects of anticarcinogenic monoterpenes on phase II hepatic metabolizing enzymes (1993)

The monocyclic monoterpenoid compounds limonene and sobrerol have anticarcinogenic activity when fed during the initiation stage of dimethylbenz[a]anthracene (DMBA)-induced rat mammary carcinogenesis. Here we investigated the potential roles of hepatic glutathione-S-transferase (GST; EC 2.5.1.18) and uridine diphosphoglucuronosyl transferase (UDPGT; EC 2.4.1.17) in monoterpene-mediated chemoprevention. Diets containing the isoeffective anticarcinogenic terpenes, 5% limonene or 1% sobrerol, elevated hepatic GST activity > 2-fold when measured using the general substrate 1-chloro-2,4-dinitrobenzene and 3,4-dichloronitrobenzene for the GST dimer 3-3. However, there were no significant changes in hepatic GST activity when 1,2-epoxy-3-(p-nitrophenoxy)propane was used. We found that both terpene diets increased GST affinity-purified protein 1.5-fold and the HPLC subunit profile. Liver GST subunit 3 had the greatest increase followed by 1 and 4 with no change in subunit 2. Both terpene diets significantly increased the activity of the methylcholanthrene-inducible and the phenobarbital-inducible UDPGT isozymes. We propose that much of the anticarcinogenic activity of these monocyclic monoterpenes during the initiation phase of DMBA carcinogenesis is mediated through the induction of the hepatic detoxification enzymes GST and UDPGT.
Phase I/II trial of preoperative thermoradiotherapy in the treatment of urinary bladder cancer (1994)

Between April 1984 and September 1988, preoperative radiotherapy or thermoradiotherapy was administered to 49 patients with bladder cancer (T1-4N0M0; UICC classification, 1987). Twenty-one patients were preoperatively treated by radiotherapy alone, with 4 Gy per fraction and three fractions per week to a total dose of 24 Gy (TDF = 53, group 1). The other 28 patients were treated by the same radiotherapy regimen in combination with hyperthermia (group 2). Regional hyperthermia was administered for 35–60 min immediately after irradiation (two sessions per week to a total of four sessions) using an 8 MHz RF capacitive heating device. Group 2 was divided into group 2 (high), in which the average intravesical temperature (Tav) was >41·5°C, which was the mean value, and group 2 (low) with a Tav <41·5°C. Group 2 (high) showed a significantly higher incidence of down-staging and tumour degeneration than both group 1 and group 2 (low). In addition, the local recurrence rate was lower and survival time was longer in group 2 than in group 1, although not significantly so. In particular, the patients with T3–4 or grade 3 bladder cancer in group 2 had a longer average survival than those in group 1, although the difference was not significant. The toxicity accosiated with hyperthermia was pain during treatment, and complications were not serious.
900-1800 nm, all-fiber nanosecond pulse source pumped by a low-power laser diode (2005)

25-mW-output-power Er/Brillouin-oscillator, a conventional dispersion-shifted fiber, and introduced bending losses are the simplest way to realize nanosecond, all-fiber laser sources operating in 900-1800 nm. Expanding evolution of the spectrum kicked off by multi-cascade-Brillouin-random-process is reported.
Clonidine for smoking cessation (2004)

Based on a small number of trials, in which there are potential sources of bias, clonidine is effective in promoting smoking cessation. Prominent side-effects limit the usefulness of clonidine for smoking cessation.
Uses of Eye-Tracking Data in Second Language Sentence Processing Research (2010)

When hearing or reading words and sentences in a second language (L2), we face many uncertainties about how the people and objects referred to are connected to one another. So what do we do under these conditions of uncertainty? Because relatively proficient L2 speakers have access to the grammar and lexicon of each language when comprehending words and sentences or when planning spoken utterances, and because the recent research suggests that these linguistic systems are not entirely independent, there is a critical question about how the knowledge of two languages affects basic aspects of language processing. In this article, I review how eye-tracking methodology has been used as a tool to address this question. I begin by discussing why eye movements are a useful methodology in language processing research, and I provide a description of one experimental paradigm developed to explore eye movements during reading. Second, I present recent developments in the use of eye tracking to study L2 spoken-language comprehension. I also highlight the importance of using multiple measures of online sentence processing by discussing results obtained using a moving window task and eye-tracking records while L2 speakers read syntactically ambiguous relative clauses. Next, I discuss research investigating syntactic processing when L2 speakers process mixed language. I end with suggestions for future research directions.
Engineering support vector machine kernels that recognize translation initiation sites (2000)

The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.
Cloning and expression in Escherichia coli of genetic determinants for production of and immunity to microcin E492 from Klebsiella pneumoniae (1997)

Microcin E492 is a polypeptide antibiotic that is produced and excreted by Klebsiella pneumoniae RYC492. The genetic determinants for microcin synthesis and immunity were cloned in Escherichia coli VCS257 into the cosmid vector pHC79, starting from total DNA of K. pneumoniae RYC492. The microcin E492 expressed in E. coli had the same properties as that of K. pneumoniae, i.e., the same molecular weight, the ability to form ionic channels in planar phospholipid bilayers, and essentially identical biological properties. Microcin E492 expression in E. coli, like that in K. pneumoniae, was mainly in the exponential phase of growth, declining in the stationary phase. The immunity determinant was subcloned into the same vector, and its expression was found to disappear in the stationary phase. This phenomenon is not dependent on rpoS, the stationary-phase sigma factor.
Biochemistry of homologous recombination in Escherichia coli (1994)

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.
Emergence of fluoroquinolone-resistant Escherichia coli at a cancer center (1994)

Prophylactic treatment with fluoroquinolones of patients with profound neutropenia has been found to be useful for preventing gram-negative bacteremia and has become a standard preventive-therapy strategy in many cancer centers, but the development of bacterial resistance is a cause of concern. During the past few years, we have observed an increasing number of patients with leukemia from whom fluoroquinolone-resistant strains of Escherichia coli were isolated. The increase was significant in this patient population, and among patients with other underlying diseases, the rates of isolation of such strains per number of discharges were significantly lower and did not increase. Most of the leukemia case patients (16 of 19) had been pretreated with an oral quinolone (ofloxacin), with cumulative doses until the first isolation of a resistant E. coli strain ranging from 0 to 97.8 g (median, 14.4 g). Repeated isolation of such strains was seen in 8 of 17 patients during a follow-up period of > or = 4 weeks and in 1 of 6 patients during a follow-up period of > or = 16 weeks. Ten patients developed bacteremia (mortality, 1 of 10). On the basis of the number of patients with leukemia admitted to the hematology-oncology service, the incidence of bacteremia caused by fluoroquinolone-resistant E. coli increased from < 0.5% in 1988-1989 and 0.8% in 1990-1991 to 4.5% in 1992-1993 (P < 0.01). MICs for nine isolates obtained from cultures of blood from different patients ranged between 8 and 16 microgram/ml (ciprofloxacin and PD 131628), 8 and 32 microgram/ml (ofloxacin and BAY Y 3118), and 16 and 32 microgram/ml (sparfloxacin) and indicated resistance to trimethoprim-sulfamethoxazole, ampicillin, doxycycline, and chloramphenicol. Of nine isolates obtained from cultures of blood from different patients and that were subjected to genomic DNA typing by pulsed-field gel electrophoresis of XbaI digests, seven were typeable. Among these, four different genotypes were identified, suggesting both the independent development and the horizontal spread of resistant clones of E. coli.