gebhart/patrepeval huggingface dataset:
Globin gene transcripts can utilize histone gene 3′ end processing signals (1986)

Deletion of the poly(A) site from the human alpha globin gene results in a defective gene that produces very little stable mRNA as compared to the intact gene, presumably due to the instability of the mRNA. However, if the Alpha poly(A) site is replaced by mouse histone H4 3' end processing signals, significant levels of hybrid alpha/H4 mRNA are obtained and the transcripts formed are cytoplasmic and poly(A)-. When both mouse histone 3' end processing signals and the alpha globin poly(A) site signals are placed in tandem after the alpha globin gene promoter and coding sequence, the alpha poly(A) site signals are utilized exclusively. These results show that the histone 3' end processing signals can function independently of the histone promoter and the transcripts which are normally polyadenylated (alpha globin) can be stabilized by a poly(A)- histone mRNA 3' terminus. Furthermore, these results show that the histone 3' end processing signals are less efficient than the alpha globin poly(A) site signals, if the two are placed in direct competition.
Defining the Vulnerable Period for Re-Establishment of Clostridium difficile Colonization after Treatment of C. difficile Infection with Oral Vancomycin or Metronidazole (2013)

These data demonstrate that there is a vulnerable period for re-establishment of C. difficile colonization after CDI treatment that begins within a few days after discontinuation of treatment and extends for about 3 weeks in most patients.
Lipid profiling identifies a triacylglycerol signature of insulin resistance and improves diabetes prediction in humans (2011)

Dyslipidemia is an independent risk factor for type 2 diabetes, although exactly which of the many plasma lipids contribute to this remains unclear. We therefore investigated whether lipid profiling can inform diabetes prediction by performing liquid chromatography/mass spectrometry-based lipid profiling in 189 individuals who developed type 2 diabetes and 189 matched disease-free individuals, with over 12 years of follow up in the Framingham Heart Study. We found that lipids of lower carbon number and double bond content were associated with an increased risk of diabetes, whereas lipids of higher carbon number and double bond content were associated with decreased risk. This pattern was strongest for triacylglycerols (TAGs) and persisted after multivariable adjustment for age, sex, BMI, fasting glucose, fasting insulin, total triglycerides, and HDL cholesterol. A combination of 2 TAGs further improved diabetes prediction. To explore potential mechanisms that modulate the distribution of plasma lipids, we performed lipid profiling during oral glucose tolerance testing, pharmacologic interventions, and acute exercise testing. Levels of TAGs associated with increased risk for diabetes decreased in response to insulin action and were elevated in the setting of insulin resistance. Conversely, levels of TAGs associated with decreased diabetes risk rose in response to insulin and were poorly correlated with insulin resistance. These studies identify a relationship between lipid acyl chain content and diabetes risk and demonstrate how lipid profiling could aid in clinical risk assessment.
Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells (2001)

Microsatellite instability (MSI) caused by deficient DNA mismatch-repair functions is a hallmark of cancers associated with the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome but is also found in about 15% of all sporadic tumors. Most affected microsatellites reside in untranslated intergenic or intronic sequences. However, recently few genes with coding microsatellites were also shown to be mutational targets in MSI-positive cancers and might represent important mutation targets in their pathogenesis. The systematic identification of such genes and the analysis of their mutation frequency in MSI-positive cancers might thus reveal major clues to their functional role in MSI-associated carcinogenesis. We therefore initiated a systematic database search in 33,595 distinctly annotated human genes and identified 17,654 potentially coding mononucleotide repeats (cMNRs) and 2,028 coding dinucleotide repeats (cDNRs), which consist of n > or = 6 and n > or = 4 repeat units, respectively. Expression pattern and mutation frequency of 19 of these genes with the longest repeats were compared between DNA mismatch repair-deficient (MSI(+)) and proficient (MSS) cancer cells. Instability frequencies in these coding microsatellite genes ranged from 10% to 100% in MSI-H tumor cells, whereas MSS cancer cells did not show mutations. RT-PCR analysis further showed that most of the affected genes (10/15) were highly expressed in tumor cells. The approach outlined here identified a new set of genes frequently affected by mutations in MSI-positive tumor cells. It will lead to novel and highly specific diagnostic and therapeutic targets for microsatellite unstable cancers.
Identification and characterization of a novel factor XIIa inhibitor in the hematophagous insect, Triatoma infestans (Hemiptera: Reduviidae) (2004)

Recently, we have cloned several Kazal-type serine protease inhibitors from the midgut of the Triatoma infestans bug. A single gene composed of multi Kazal-type domains, in tandem, encodes these inhibitors. In this work, we describe the purification and characterization of recombinant infestins 3-4 and 4, which are potent factor XIIa inhibitors (KI=67 pM and 128 pM, respectively). We also identified the first native factor XIIa inhibitor from a hematophagous insect. The factor XIIa inhibitory activity of infestin 4 demonstrates extremely efficient anticoagulant activity, prolonging activated partial thromboplastin time by approximately 3 times. Our results suggest that infestins perform a very important role in the T. infestans midgut during meal acquisition and digestion by controlling blood coagulation by means of inhibiting thrombin and factor XIIa.
Long-range ordered lines of self-assembled Ge islands on a flat Si (001) surface (2000)

Self-assembled growth in combination with prepatterning yields ordered lines of Ge islands on a planar Si (001) surface. The self-assembled Ge nanostructures are grown on top of a 15-period Si/SiGe superlattice, which is deposited on a prepatterned Si substrate. The pattern consists of 10 nm deep trenches with a period of 250 nm. The superlattice translates the surface modulation of the substrate into a strain-field modulation at the growth front of the superlattice. This strain field modulation provides the template for the ordered nucleation of self-assembled Ge islands. Our method gives rise to the long-range ordering of perfectly passivated nanostructures and can in principle be applied to any other strained material system.
The single-mode condition for semiconductor rib waveguides with large cross section (1998)

A comparison of the single-mode condition for semiconductor rib waveguides with large cross section obtained by the effective index method and the corrected formula proposed by Soref et al. [see IEEE Journal of Quantum Electronics, vol. 27, p. 1971, 1991] with experimental data is carried out. It is found that the effective index method is in a better agreement with Rickman's experimental data than the modified version. Moreover a stronger condition is proposed for single-mode design purposes.
Heterosubtypic Protection against Pathogenic Human and Avian Influenza Viruses via In Vivo Electroporation of Synthetic Consensus DNA Antigens (2008)

By combining several consensus influenza antigens with in vivo electroporation, we demonstrate that these antigens induce both protective cellular and humoral immune responses in mice, ferrets and non-human primates. We also demonstrate the ability of these antigens to protect from both morbidity and mortality in a ferret model of HPAI, in both the presence and absence of neutralizing antibody, which will be critical in responding to the antigenic drift that will likely occur before these viruses cross the species barrier to humans.
Xylanase production by ultra violet induced variants of Streptomyces fradiae SCF-5. (1978)

Vegetative cells (VC) and spores of Streptomyces fradiae SCF-5 were exposed to UV irradiation for 0-120 s; their ability to degrade xylan was then investigated. At shorter exposure times, VC were more resistant to UV than the spores; at longer periods of exposure the VC were inactivated faster than the spores. The irradiated strains, when grown in basal medium containing wheat bran (1.0%) and glucose (0.1%) produced 0.19-0.2 units ml---1 of xylanase, compared to 0.05-0.06 units ml---1 produced by the parent strain. Chromatographic analysis of sugars formed by hydrolysis of xylan by the culture fluids of 3 strains with high xylanase yields over 4 to 72 h indicated differences in the quality of xylanase produced by parent and variant strains. High xylanase yield variants could grow on natural xylan substrates (wheat bran and paddy straw) producing extracellular xylanase but little cell-bound glucose isomerase.
Slepian-Wolf coded nested quantization (SWC-NQ) for Wyner-Ziv coding: performance analysis and code design (2004)

This paper examines the high-rate performance of low-dimensional nested lattice quantizers for the quadratic Gaussian Wyner-Ziv problem, using a pair of nested lattices with the same dimensionality. As the rate increases, the gap increases between the performances of low dimensional nested lattice quantizers and the Wyner-Ziv rate-distortion function. This gap is due to the relatively weak channel coding component (or coarse lattice) in the nested lattice pair. To enhance the lattice channel code and boost the overall performance, Slepian-Wolf coding is applied to the quantization indices to achieve further compression. Thereby a Wyner-Ziv coding paradigm is introduced using Slepian-Wolf coded nested lattice quantization (SWC-NQ). Theoretical analysis and simulation results show that, for the quadratic Gaussian source and at high rate, SWC-NQ performs the same as traditional entropy-constrained lattice quantization with side information available at both the encoder and decoder.
Resistance exercise and strong healthy children: safe when done right! (2008)

Weight lifting in children and youth is often viewed as a potentially harmful activity that could result in damage to bones, connective tissue, and muscle. Reviews, such as the one appearing in this issue of the journal by Behm et al. (Appl. Physiol. Metab. Nutr. 33: this issue), show that the balance of evidence indicates that weight lifting in pediatric populations is safe. Importantly, weight lifting, when performed in a safe and age-appropriate manner, is very beneficial on a number of health fronts, including strength and balance, self-esteem, and reducing cardiovascular risks. This is an understudied area that is still lacking in key areas of research to establish efficacy, dose-response relationships, and other health benefits.
Determination of UVA protection factors using the persistent pigment darkening (PPD) as the end point (2000)

The calibration procedure proposed shows threshold PPD, used as an end point in a UVA-PF test method, to be a reliable endogenous dosimeter for UVA radiation that enters the skin.
Frequent overexpression of aurora B kinase, a novel drug target, in non–small cell lung carcinoma patients (2006)

The serine/threonine protein kinase aurora B, a key regulator of mitosis, is emerging as a novel drug target for cancer treatment. Aurora B overexpression has been previously documented by immunohistochemistry in several types of human tumors. We assessed aurora B expression in a series of 160 non-small cell lung cancer (NSCLC) samples (60% stage I, 21% stage II, 11% stage III, and 8% stage IV). In addition, we determined the expression of survivin and p16, two molecules also involved in cell cycle control. Aurora B was expressed selectively in tumor cells compared with normal epithelium. Aurora B expression was significantly correlated with expression of survivin in the nucleus (P < 0.0001), but not with expression of p16 (P = 0.134). High aurora B expression levels were significantly associated with older age (P = 0.012), male sex (P = 0.013), squamous cell carcinoma histology (P = 0.001), poor tumor differentiation grade (P = 0.007), and lymph node invasion (P = 0.037), in the subset of radically resected patients in our series. In addition, aurora B expression predicted shorter survival for the patients with adenocarcinoma histology, at both univariate (P = 0.020) and multivariate (P = 0.012) analysis. Survivin expression levels were neither associated with patient clinicopathologic characteristics nor with survival. However, expression of survivin in the nucleus was preferentially detected in stage I and II than in stage III and IV (P = 0.007) in the overall series of NSCLC samples. Taken together, our results suggest that aurora B may represent a valid target in NSCLC.
Expression of Norwalk virus capsid protein in transgenic tobacco and potato and its oral immunogenicity in mice. (1996)

Alternatives to cell culture systems for production of recombinant proteins could make very safe vaccines at a lower cost. We have used genetically engineered plants for expression of candidate vaccine antigens with the goal of using the edible plant organs for economical delivery of oral vaccines. Transgenic tobacco and potato plants were created that express the capsid protein of Norwalk virus, a calicivirus that causes epidemic acute gastroenteritis in humans. The capsid protein could be extracted from tobacco leaves in the form of 38-nm Norwalk virus-like particles. Recombinant Norwalk virus-like particle (rNV) was previously recovered when the same gene was expressed in recombinant baculovirus-infected insect cells. The capsid protein expressed in tobacco leaves and potato tubers cosedimented in sucrose gradients with insect cell-derived rNV and appeared identical to insect cell-derived rNV on immunoblots of SDS/polyacrylamide gels. The plant-expressed rNV was orally immunogenic in mice. Extracts of tobacco leaf expressing rNV were given to CD1 mice by gavage, and the treated mice developed both serum IgG and secretory IgA specific for rNV. Furthermore, when potato tubers expressing rNV were fed directly to mice, they developed serum IgG specific for rNV. These results indicate the potential usefulness of plants for production and delivery of edible vaccines. This is an appropriate technology for developing countries where vaccines are urgently needed.
MEMS-Based Power Generation Techniques for Implantable Biosensing Applications (2011)

Implantable biosensing is attractive for both medical monitoring and diagnostic applications. It is possible to monitor phenomena such as physical loads on joints or implants, vital signs, or osseointegration in vivo and in real time. Microelectromechanical (MEMS)-based generation techniques can allow for the autonomous operation of implantable biosensors by generating electrical power to replace or supplement existing battery-based power systems. By supplementing existing battery-based power systems for implantable biosensors, the operational lifetime of the sensor is increased. In addition, the potential for a greater amount of available power allows additional components to be added to the biosensing module, such as computational and wireless and components, improving functionality and performance of the biosensor. Photovoltaic, thermovoltaic, micro fuel cell, electrostatic, electromagnetic, and piezoelectric based generation schemes are evaluated in this paper for applicability for implantable biosensing. MEMS-based generation techniques that harvest ambient energy, such as vibration, are much better suited for implantable biosensing applications than fuel-based approaches, producing up to milliwatts of electrical power. High power density MEMS-based approaches, such as piezoelectric and electromagnetic schemes, allow for supplemental and replacement power schemes for biosensing applications to improve device capabilities and performance. In addition, this may allow for the biosensor to be further miniaturized, reducing the need for relatively large batteries with respect to device size. This would cause the implanted biosensor to be less invasive, increasing the quality of care received by the patient.
Answering table augmentation queries from unstructured lists on the web (2009)

We present the design of a system for assembling a table from a few example rows by harnessing the huge corpus of information-rich but unstructured lists on the web. We developed a totally unsupervised end to end approach which given the sample query rows --- (a) retrieves HTML lists relevant to the query from a pre-indexed crawl of web lists, (b) segments the list records and maps the segments to the query schema using a statistical model, (c) consolidates the results from multiple lists into a unified merged table, (d) and presents to the user the consolidated records ranked by their estimated membership in the target relation. The key challenges in this task include construction of new rows from very few examples, and an abundance of noisy and irrelevant lists that swamp the consolidation and ranking of rows. We propose modifications to statistical record segmentation models, and present novel consolidation and ranking techniques that can process input tables of arbitrary schema without requiring any human supervision. Experiments with Wikipedia target tables and 16 million unstructured lists show that even with just three sample rows, our system is very effective at recreating Wikipedia tables, with a mean runtime of around 20s.
Radiofrequency Lesion Generation and lts Effect on Tissue Impedance (1988)

The method of radiofrequency heat lesion generation is reviewed with specific reference to the dorsal root entry zone. Experimental data on the impedance of electrolytic media as a function of temperature are reported, and their relation to what should be observed during radiofrequency lesioning in the body is commented upon. The future utility of impedance monitoring is discussed as well as possible implications of bipolar lesion electrode systems.
Understanding CRY2 interactions for optical control of intracellular signaling (2017)

Arabidopsis cryptochrome 2 (CRY2) can simultaneously undergo light-dependent CRY2-CRY2 homo-oligomerization and CRY2-CIB1 hetero-dimerization, both of which have been widely used to optically control intracellular processes. Applications using CRY2-CIB1 interaction desire minimal CRY2 homo-oligomerization to avoid unintended complications, while those utilizing CRY2-CRY2 interaction prefer robust homo-oligomerization. However, selecting the type of CRY2 interaction has not been possible as the molecular mechanisms underlying CRY2 interactions﻿ are unknown. Here we report CRY2-CIB1 and CRY2-CRY2 interactions are governed by well-separated protein interfaces at the two termini of CRY2. N-terminal charges are critical for CRY2-CIB1 interaction. Moreover, two C-terminal charges impact CRY2 homo-oligomerization, with positive charges facilitating oligomerization and negative charges inhibiting it. By engineering C-terminal charges, we develop CRY2high and CRY2low with elevated or suppressed oligomerization respectively, which we use to tune the levels of Raf/MEK/ERK signaling. These results contribute to our understanding of the mechanisms underlying light-induced CRY2 interactions and enhance the controllability of CRY2-based optogenetic systems.Cryptochrome 2 (CRY2) can form light-regulated CRY2-CRY2 homo-oligomers or CRY2-CIB1 hetero-dimers, but modulating these interactions is difficult owing to the lack of interaction mechanism. Here the authors identify the interactions facilitating homo-oligomers and introduce mutations to create low and high oligomerization versions.
From Cd-Rich to Se-Rich − the Manipulation of CdSe Nanocrystal Surface Stoichiometry (2007)

We report a protocol for manipulating the surface composition of CdSe nanocrystals. By combining the successive ion layer adhesion and reaction (SILAR) method developed by Li et al. J. Am. Chem. Soc. 2003, 125, 12567 with a phosphine-free selenium precursor, the surface stoichiometry of CdSe can be tunably altered from Cd- to Se-rich. By changing the overall surface stoichiometry, we demonstrate ligand binding to specific surface sites. Tertiary phosphines produce a dramatic enhancement in photoluminescence quantum yield of CdSe particles with Se-rich surfaces but have little effect on Cd-rich surfaces. Unpassivated selenium surface sites are also shown to be a cause of the photobrightening behavior of CdSe nanocrystals.
CD4+ T Cells of Schistosomiasis Naturally Resistant Individuals Living in an Endemic Area Produce Interferon‐γ and Tumour Necrosis Factor‐α in Response to The Recombinant 14kdaSchistosoma mansoni Fatty Acid‐Binding Protein (2000)

Cellular immune responses to recombinant (r) Sm14 were examined in chronic, treated patients and uninfected individuals living in an endemic area for schistosomiasis. The lymphocyte proliferative responses and cytokine profile to this antigen were evaluated. Peripheral blood mononuclear cells (PBMC) of all groups studied proliferated to rSm14. However, the highest proliferation index to rSm14 was detected in uninfected endemic normal (EN) individuals who are naturally resistant to schistosomiasis. Regarding the cytokines produced, the levels of interleukin (IL)-5 and IL-10, known as Th2 cytokines, were not statistically different among all groups studied. In contrast, interferon (IFN)-gamma and tumour necrosis factor (TNF)-alpha were produced in significantly higher amounts by PBMC of EN individuals following rSm14 stimulation. Additionally, we have determined by flow cytometry that CD4+ T cells from these individuals are the main lymphocyte subpopulation producing IFN-gamma and TNF-alpha. Moreover, we have used rIL-10 or rIFN-gamma, or monoclonal antibodies (MoAb) against these two cytokines to determine their role on cellular reactivity to rSm14. Exogenous IL-10 suppressed T-cell proliferation and neutralization of endogenous IL-10 restored lymphocyte activation and enhanced IFN-gamma and TNF-alpha production in chronically infected patients. In contrast, the addition of anti-IFN-gamma totally abrogated the PBMC proliferation within the EN group. This study demonstrated that IL-10 is an important cytokine down-regulating T-cell responses in chronic schistosomiasis, whereas lymphocyte proliferation in the uninfected resistant group is dependent on IFN-gamma. Taken together these results suggest that Th1 type of immune response induced in EN individuals to a specific schistosome antigen might be associated with resistance to infection and also highlighted the importance of Sm14 as a potential vaccine candidate.
Heteroepitaxy of GaN on Si(111) realized with a coincident-interface AlN/β-Si3N4(0001) double-buffer structure (2003)

We present a stacked buffer mechanism for heteroepitaxial growth with large lattice mismatch. The stacked buffer consists of constituent layers, which can form coincident lattices at layer/layer and layer/substrate interfaces. For the case of GaN-on-Si(111) heteroepitaxy, we utilize the 1:2 and 5:2 coincident lattices formed at the β-Si3N4(0001)/Si(111) and AlN(0001)/β-Si3N4(0001) interfaces, respectively, to facilitate the double-buffer layer for GaN-on-Si heteroepitaxial growth. By using this buffer technique, we resolve the issue of autodoping resulting from Si outdiffusion when grown with a single AlN(0001) buffer. As a result, the epitaxial quality of GaN film is also significantly improved.
A Highly Robust Audio Fingerprinting System. (2002)

[TODO] Add abstract here.