gebhart/patrepeval huggingface dataset:
Scoliosis: Comparative Analysis of Surgery vs. Brace Treatment (2011)

The following is the introduction of this article: The spine, or spinal column, as it is also called, is a complex structure made up of 33 vertebrae (bone segments) arranged vertically in succession from just below the skull to the tailbone. The entire column is broken up into various classes of vertebrae named, from superior to inferior, as cervical, thoracic, lumbar, sacral, and coccygeal. Different forms of spinal deformities that can occur include kyphosis, lordosis and scoliosis (Neuwirth and Osborn 2001). Scoliosis is defined simply in medical terms as a lateral three-dimensional irregular curvature of the spine. The curvature as seen from the back of the person can be described as an “s” shaped bend or a “c” shaped bend. The spinal curves are measured by degrees of curvature and depending on the severity of the degree of curvature, an appropriate treatment method will be determined. Scoliosis curvatures do not retain a status quo over time. If not treated properly, the curves tend to progressively worsen, causing pain and discomfort to the diseased party. In this paper, different methods that are used in treating scoliosis are discussed including the different types of braces that are used and the various forms of surgeries that are performed in such cases.
Corticothalamic activation modulates thalamic firing through glutamate "metabotropic" receptors. (1992)

The mammalian thalamus forms an obligatory relay for nearly all sensory information that reaches the cerebral cortex. The transmission of sensory information by the thalamus varies in a state-dependent manner, such that during slow wave sleep or drowsiness thalamic responsiveness is markedly reduced, whereas during the waking, attentive state transmission is enhanced. Although activation of brainstem inputs to thalamic neurons has long been assumed to underlie this gating of sensory transfer through the thalamus, numerically the largest input to thalamic relay neurons derives from layer VI cells of the cerebral cortex. Here we report that activation of corticothalamic fibers causes a prolonged excitatory postsynaptic potential in guinea pig dorsal lateral geniculate relay neurons resulting from the reduction of a potassium conductance, consistent with the activation of glutamatergic "metabotropic" receptors. This slow depolarization can switch firing of thalamic neurons from the burst firing mode, which is prevalent during slow wave sleep, to the single spike mode, which is prevalent during waking, thereby facilitating transmission of sensory information through the thalamus. This prolonged enhancement of thalamic transfer may allow the cerebral cortex to gate or control selective fields of sensory inputs in a manner that facilitates arousal, attention, and cognition.
Comparison of Selection Methods for the Development of White‐Seeded Lines from Red × White Soft Winter Wheat Crosses (2008)

There has been increasing interest in developing soft white winter wheat ( Triticum aestivum L.) cultivars for areas that have traditionally grown only soft red winter wheat. To develop white wheat segregates in a red wheat breeding program requires deliberate breeding decisions. The objectives of this study were to assess differences in agronomic, disease, and milling and baking quality traits between red and white progeny in 11 red × white crosses and to determine the optimal time and method for identifying white segregates from red × white crosses. Red and white progeny from the 11 populations were evaluated in replicated experiments at three locations in 2005–2006. White progeny produced significantly ( p &lt; 0.05) lower grain yields than red progeny in two of five environments studied. Deoxynivalenol level was significantly ( p &lt; 0.05) higher in white than in red progeny in the three environments in which it was measured. Flour yield, flour lactic acid solvent retention capacity, and softness equivalent were significantly ( p &lt; 0.05) lower for white progeny than for red progeny. To determine the optimal generation for selection of white lines, early‐generation bulk selection was compared with single seed descent in three populations at two locations. Although there were significant ( p &lt; 0.05) differences between selection methods within populations, neither breeding method was consistently superior across the three populations. Simulated selection of superior white lines based on agronomic and milling and baking quality showed no significant differences between the selection methods.
Role of the mTOR complex 1 pathway in the in vivo maintenance of the intestinal mucosa by oral intake of amino acids (2011)

These results indicate that the mTORC1 pathway plays a crucial role in the in vivo maintenance of the intestinal mucosa by the oral intake of amino acids.
Substrate recognition by the 2 micron circle site-specific recombinase: effect of mutations within the symmetry elements of the minimal substrate. (1986)

The minimal substrate for the 2 microns circle site-specific recombinase FLP consists of a nearly perfect 13-base-pair dyad symmetry with an 8-base-pair core. By using a series of chemically synthesized FLP substrates in in vitro FLP recombination and FLP-binding assays, we have identified four positions within each of the symmetry elements that are important contact points for the FLP protein. Furthermore, the binding and recombination data provide evidence for cooperativity between the two symmetry elements of a substrate and between the symmetry elements of two partner substrates during FLP recombination.
HLA class II transgenic mice as models of human diseases (1999)

Predisposition to develop various autoimmune disorders has been associated with certain HLA class II molecules but there is a lack of information on the pathophysiological role of HLA genes in conferring susceptibility. Various experimental animal models of autoimmune disease have been studied to address the role of immune response genes. To study the interactions involved between class II molecules (DQ and DR) and define the immunologic mechanisms in various diseases, we generated HLA-DR and DQ transgenic mice that lacked endogenous class II molecules. The HLA molecules in these mice are expressed on the cell surface and can positively select CD4+ T cells expressing various V beta T-cell receptors (TCR). A peripheral tolerance is maintained to transgenic HLA molecules thus indicating that these molecules act as self. Mouse co-stimulatory and accessory molecules can interact with the HLA-peptide-TCR complex leading to efficient T-cell activation. In this review, we describe immunogenetic models for human diseases using these transgenic mice. Our studies show that HLA class II transgene-restricted T cells recognize the immunodominant antigens and peptide epitopes, similar to HLA class II-restricted human T cells. Thus these mice provide powerful tools to understand the role of HLA class II molecules in predisposition and onset of human diseases and to develop immunotherapy and vaccines.
The Immune System Strikes Back: Cellular Immune Responses against Indoleamine 2,3-dioxygenase (2009)

IDO may serve as an important and widely applicable target for anti-cancer immunotherapeutic strategies. Furthermore, as emerging evidence suggests that IDO constitutes a significant counter-regulatory mechanism induced by pro-inflammatory signals, IDO-based immunotherapy holds the promise to boost anti-cancer immunotherapy in general.
An acoustic aneurysm-detector. (1987)

Intracranial aneurysms have a high prevalence in the adult population; and if they rupture, significant morbidity almost always ensues. However, pulsatile blood flow through aneurysms produces vibrational sound patterns that may be detected extracranially. Thus, an acoustic aneurysm-detector has been developed to detect the sounds produced by intracranial aneurysms prior to rupture. The design is based on the utilization of a hydrophone for signal detection and computational signal processing for signal extraction. Data are examined in the time domain, the frequency domain, and the time-frequency plane. Examples are presented from an animal model and from a patient with a known aneurysm.
Synthesis of several pyrimidine l-nucleoside analogues as potential antiviral agents (1995)

β-l-5-Iodo-2′-deoxyuridine (β-l-IUdR, 7) and 1-[(β-l-arabinofuranosyl)-E-5-(2-bromovinyl)]uracil (β-l-BV-ara-U, 10) have been synthesized via a multi-step synthesis from l-arabinose. 2′,3′-Dideoxy-β-l-5-azacytidine (18), 2′,3′-dideoxy-β-l-2-thiocytidine (20) and their respective α-anomers, compounds 19 and 21, also were synthesized by direct coupling of 1-O-acetyl-5-O-(tert-butyldimethylsilyl)-2,3-dideoxy-l-ribofuranose (13) with the corresponding silylated bases, in the presence of EtAlCl2 in CH2Cl2, followed by separation of the α- and β-isomers and deblocking of the 5′-protecting groups. In addition, 2′,3′-dideoxy-β-l-5-fluorocytidine (34), a potent anti-HIV and anti-HBV agent, was synthesized by an alternative methodology from 2′,3′-dideoxy-β-l-5-fluorouridine (31) via a 4-triazolylpyrimidinone intermediate. These l-nucleoside analogues were tested in vitro against HIV, HBV, HSV-1, and HSV-2. Among these compounds, 2′,3′-dideoxy-β-l-5-azacytidine (18) was found to show significant activity against HBV in vitro at approximately the same level as 2′,3′-dideoxy-β-d-cytidine (ddC), which is a known potent anti-HBV agent.
p53 regulates cell survival by inhibiting PIK3CA in squamous cell carcinomas (2002)

Interactions between the p53 and PI3K/AKT pathways play a significant role in the determination of cell death/survival. In benign cells these pathways are interrelated through the transcriptional regulation of PTEN by p53, which is required for p53-mediated apoptosis. PTEN exerts its effects by decreasing the phosphorylated AKT fraction, thereby diminishing prosurvival activities. However, the link between these pathways in cancer is not known. In this study, PIK3CA, encoding the p110alpha catalytic subunit of PI3K, is identified as an oncogene involved in upper aerodigestive tract (UADT) carcinomas. Simultaneous abnormalities in both pathways are rare in primary tumors, suggesting that amplification of PIK3CA and mutation of p53 are mutually exclusive events and either event is able to promote a malignant phenotype. Moreover, the negative effect of p53 induction on cell survival involves the transcriptional inhibition of PIK3CA that is independent of PTEN activity, as PTEN is not expressed in the primary tumors. Conversely, constitutive activation of PIK3CA results in resistance to p53-related apoptosis in PTEN deficient cells. Thus, p53 regulates cell survival by inhibiting the PI3K/AKT prosurvival signal independent of PTEN in epithelial tumors. This inhibition is required for p53-mediated apoptosis in malignant cells.
Tunable large resonant absorption in a midinfrared graphene Salisbury screen (2014)

The optical absorption properties of periodically patterned graphene plasmonic resonators are studied experimentally as the graphene sheet is placed near a metallic reflector. By varying the size and carrier density of the graphene, the parameters for achieving a surface impedance closely matched to free-space $({Z}_{0}\phantom{\rule{0.16em}{0ex}}=\phantom{\rule{0.16em}{0ex}}377\phantom{\rule{0.16em}{0ex}}\ensuremath{\Omega})$ are determined and shown to result in 24.5% total optical absorption in the graphene sheet. Theoretical analysis shows that complete absorption is achievable with higher doping or lower loss. This geometry, known as a Salisbury screen, provides an efficient means of light coupling to the highly confined graphene plasmonic modes for future optoelectronic applications.
A comparative study of pilot-based channel estimators for wireless OFDM (1996)

This report deals with pilot-based channel estimation in wireless OFDM systems. We assume that the receiver is able to use all transmitted pilots, which is the case in broadcasting and in the downlink of a multiuser system. Four estimators (of which two have been proposed in the literature) are compared, both in terms of mean-squared error and bit-error rates. In the latter case, we simulate a multiuser system which incorporates channel coding. The channel estimation is a two-dimensional problem (time and frequency), and both separable and non-separable estimators are investigated. We design low-rank approximations of these estimators, and compare the performance at given complexities. The comparison shows that the use of separable estimators increases the performance substantially, compared to non-separable estimators with the same complexity. For the scenario investigated in this report the performance is further improved by applying low-rank approximations to separable estimators.
Protection of infant rats from Haemophilus influenzae type b infection by antiserum to purified outer membrane protein a (1987)

Protein a (46,000 molecular weight [46K]) was purified from outer membranes of Haemophilus influenzae type b by a relatively simple procedure. Spontaneously shed outer membranes from a 24-h, 12-liter culture of an unencapsulated variant of strain Eag were combined with outer membranes released from the cells by Tris buffer and extracted with the nonionic detergent octylpolyoxyethylene. The extract was then subjected to open column chromatography on Sephacryl S-200 and Trisacryl-carboxymethyl to yield 7.5 mg of protein a from 180 mg of outer membrane protein. Approximately 99% of the protein in this preparation was protein a; in addition, the preparation contained 1.25% (wt/wt) lipopolysaccharide and had a residual detergent/protein ratio of 1.6:1 (wt/wt). Antibodies to the preparation were induced in rabbits by using alum as an adjuvant. As determined by immunoblotting, the great preponderance of antibodies induced were specific for protein a. However, very low levels of antibodies to several other outer membrane components, which were not apparent on gels of the pure preparation of protein a, were also induced. Preimmune and postimmune sera, after depletion of antibodies to capsular polysaccharide and lipopolysaccharide, were tested for biological activity against H. influenzae type b. Compared with preimmune serum, postimmune serum was bactericidal in vitro against strain Eag (the only strain tested) and offered significant protection (P less than 0.01) to infant rats against infection by all four strains tested, two of which had a protein a that was larger (47K) than the 46K protein a in the preparation. These results indicate that protein a should be considered as a vaccine to prevent H. influenzae type b disease.
Broad-Band Visually Evoked Potentials: Re(con)volution in Brain-Computer Interfacing (2015)

Brain-Computer Interfaces (BCIs) allow users to control devices and communicate by using brain activity only. BCIs based on broad-band visual stimulation can outperform BCIs using other stimulation paradigms. Visual stimulation with pseudo-random bit-sequences evokes specific Broad-Band Visually Evoked Potentials (BBVEPs) that can be reliably used in BCI for high-speed communication in speller applications. In this study, we report a novel paradigm for a BBVEP-based BCI that utilizes a generative framework to predict responses to broad-band stimulation sequences. In this study we designed a BBVEP-based BCI using modulated Gold codes to mark cells in a visual speller BCI. We defined a linear generative model that decomposes full responses into overlapping single-flash responses. These single-flash responses are used to predict responses to novel stimulation sequences, which in turn serve as templates for classification. The linear generative model explains on average 50% and up to 66% of the variance of responses to both seen and unseen sequences. In an online experiment, 12 participants tested a 6 × 6 matrix speller BCI. On average, an online accuracy of 86% was reached with trial lengths of 3.21 seconds. This corresponds to an Information Transfer Rate of 48 bits per minute (approximately 9 symbols per minute). This study indicates the potential to model and predict responses to broad-band stimulation. These predicted responses are proven to be well-suited as templates for a BBVEP-based BCI, thereby enabling communication and control by brain activity only.
Generation of restriction map of Enterococcus faecalis OG1 and investigation of growth requirements and regions encoding biosynthetic function (1993)

A defined synthetic medium was used to determine the amino acid requirements of Enterococcus faecalis OG1 and to demonstrate the absence of a requirement for exogenous purines or pyrimidines. Genomic libraries prepared from strain OG1 were transduced into Escherichia coli auxotrophic mutants, and cloned DNAs which complemented pyrC, pyrD, purF, purL, and guaAB mutations were identified. These and other cloned DNAs with known functions were localized on a restriction map of OG1 which was generated with SfiI (5 fragments), AscI (9 fragments), and NotI (15 fragments); the size of the OG1 chromosome was revised from a previous estimate of approximately 2,750 kb to 2,825 kb. The synthetic medium and the restriction map should be useful for studying enterococcal metabolic functions and the relationships between chromosomally encoded genes.
A fast track strategy toward highly functionalized dendrimers with different structural layers: an “onion peel approach” (2015)

A novel strategy is described for the rapid syntheses of polyhydroxylated dendrimers in which the layer by layer building blocks are different from one another. The resulting dendrimers showed no cytotoxicity.
Novel Functional Biodegradable Polymer IV:  pH-Sensitive Controlled Release of Fibroblast Growth Factor-2 from a Poly(γ-glutamic acid)-Sulfonate Matrix for Tissue Engineering (2005)

The acidic pH-sensitive controlled release of fibroblast growth factor-2 (FGF-2) from a biodegradable hydrogel without any denaturation of the FGF-2 was successfully performed by a combination of FGF-2 activity and acidic pH-sensitivity. We prepared semi-interpenetrating polymer network like hetero-gels (S72-netgels) composed of poly(gamma-glutamic acid) (gamma-PGA) and 72% sulfonated gamma-PGA (gamma-PGA-S72). S72-netgels including 36 mol % sulfonic acid (S72-netgel-36) showed wide acidic pH-sensitive deswelling properties at pH = 2.0-6.0, corresponding to the isoelectric point of carboxylic acid, because of the concentration of protons due to the neighboring sulfonic acids from the carboxylic acids. The S72-netgel-36 (the volume of hydrogel is 7.85 x 10(-2) cm3) can incorporate 280 ng of FGF-2 after 24 h immersion in Tris-HCl buffer (pH = 7.4), including 1.0 microg of FGF-2. The S72-netgel-36 still retained about 60% of the FGF-2 even after 15 days of incubation in fresh Tris-HCl buffer at 37 degrees C because of the stable interaction of FGF-2 with gamma-PGA-S72 in S72-netgel-36. The release of FGF-2 from the S72-netgel-36 was successfully controlled by alternating immersion in pH = 7.4 and acidic pH buffers. Furthermore, the FGF-2 released from the S72-netgel-36 retained its activity without denaturation because the gamma-PGA-S72 in S72-netgel-36 has a protective activity. The acidic pH-sensitive FGF-2 release property of the S72-netgel-36 without denaturation of the FGF-2 may be useful for tissue engineering fields such as neovascular treatment for ischemia and inflammation.
The association between resting heart rate, cardiovascular disease and mortality: evidence from 112,680 men and women in 12 cohorts (2012)

RHR of above 65 beats/min has a strong independent effect on premature mortality and stroke, but a lesser effect on CHD. Lifestyle and pharmaceutical regimens to reduce RHR may be beneficial for people with moderate to high levels of RHR.
Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks (2016)

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequence's saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them.
Advancing the State of the Art in Open Domain Dialog Systems through the Alexa Prize (2018)

Building open domain conversational systems that allow users to have engaging conversations on topics of their choice is a challenging task. Alexa Prize was launched in 2016 to tackle the problem of achieving natural, sustained, coherent and engaging open-domain dialogs. In the second iteration of the competition in 2018, university teams advanced the state of the art by using context in dialog models, leveraging knowledge graphs for language understanding, handling complex utterances, building statistical and hierarchical dialog managers, and leveraging model-driven signals from user responses. The 2018 competition also included the provision of a suite of tools and models to the competitors including the CoBot (conversational bot) toolkit, topic and dialog act detection models, conversation evaluators, and a sensitive content detection model so that the competing teams could focus on building knowledge-rich, coherent and engaging multi-turn dialog systems. This paper outlines the advances developed by the university teams as well as the Alexa Prize team to achieve the common goal of advancing the science of Conversational AI. We address several key open-ended problems such as conversational speech recognition, open domain natural language understanding, commonsense reasoning, statistical dialog management, and dialog evaluation. These collaborative efforts have driven improved experiences by Alexa users to an average rating of 3.61, the median duration of 2 mins 18 seconds, and average turns to 14.6, increases of 14%, 92%, 54% respectively since the launch of the 2018 competition. For conversational speech recognition, we have improved our relative Word Error Rate by 55% and our relative Entity Error Rate by 34% since the launch of the Alexa Prize. Socialbots improved in quality significantly more rapidly in 2018, in part due to the release of the CoBot toolkit.
Determination of Serum Phospholipid Metabolic Profiles by High-Performance Liquid Chromatography (1985)

Abstract A method for the separation of serum phospholipid molecular species by reversed-phase high-performance liquid chromatography is described. Total serum phospholipid extracts were hydrolyzed with phospholipase C and benzoylated, and the resulting monoglyceride, diglyceride, and ceramide derivatives were separated by using gradient elution with detection at 230nm. Both human and rat serum phospholipid extracts were examined, and the use of this method for the evaluation of serum phospholipid metabolic alterations accompanying exposure to an environmental toxicant (polybrominated biphenyls) is described.