gebhart/patrepeval huggingface dataset:
Communication between the Zinc and Tetrahydrobiopterin Binding Sites in Nitric Oxide Synthase (2014)

The nitric oxide synthase (NOS) dimer is stabilized by a Zn(2+) ion coordinated to four symmetry-related Cys residues exactly along the dimer 2-fold axis. Each of the two essential tetrahydrobiopterin (H4B) molecules in the dimer interacts directly with the heme, and each H4B molecule is ~15 Å from the Zn(2+). We have determined the crystal structures of the bovine endothelial NOS dimer oxygenase domain bound to three different pterin analogues, which reveal an intimate structural communication between the H4B and Zn(2+) sites. The binding of one of these compounds, 6-acetyl-2-amino-7,7-dimethyl-7,8-dihydro-4(3H)-pteridinone (1), to the pterin site and Zn(2+) binding are mutually exclusive. Compound 1 both directly and indirectly disrupts hydrogen bonding between key residues in the Zn(2+) binding motif, resulting in destabilization of the dimer and a complete disruption of the Zn(2+) site. Addition of excess Zn(2+) stabilizes the Zn(2+) site at the expense of weakened binding of 1. The unique structural features of 1 that disrupt the dimer interface are extra methyl groups that extend into the dimer interface and force a slight opening of the dimer, thus resulting in disruption of the Zn(2+) site. These results illustrate a very delicate balance of forces and structure at the dimer interface that must be maintained to properly form the Zn(2+), pterin, and substrate binding sites.
A new approach to image retrieval with hierarchical color clustering (1998)

After performing a thorough comparison of different quantization schemes in the RGB, HSV, YUV, and CIEL*u*v* color spaces, we propose to use color features obtained by hierarchical color clustering based on a pruned octree data structure to achieve efficient and robust image retrieval. With the proposed method, multiple color features, including the dominant color, the number of distinctive colors, and the color histogram, can be naturally integrated into one framework. A selective filtering strategy is also described to speed up the retrieval process. Retrieval examples are given to illustrate the performance of the proposed approach.
Incorporating the human hearing properties into multichannel speech enhancement (2011)

In this paper we propose perceptually motivated multichannel system for speech dereverberation and noise suppression. We modify a conventional generalized sidelobe canceler (GSC) structure by introducing perceptual weighting factor into noise cancellation loop. The purpose of this factor is to shape residual noise according to masking effects and to minimize the speech leakage. We implement the GSC structure using a delay-and-sum beamformer and blocking matrix that depends on second order statistics only. Therefore we do not require exact estimates of the channel transfer functions nor its ratios. Finally a comparative evaluation of the proposed methods is performed using objective speech quality measures. Results show that the novel method outperforms conventional one providing better speech quality.
Disruption of Imprinted Gene Methylation and Expression in Cloned Preimplantation Stage Mouse Embryos1 (2003)

Cloning by somatic cell nuclear transfer requires that epigenetic information possessed by the donor nucleus be reprogrammed to an embryonic state. Little is known, however, about this remodeling process, including when it occurs, its efficiency, and how well epigenetic markings characteristic of normal development are maintained. Examining the fate of epigenetic information associated with imprinted genes during clonal development offers one means of addressing these questions. We examined transcript abundance, allele specificity of imprinted gene expression, and parental allele-specific DNA methylation in cloned mouse blastocysts. Striking disruptions were seen in total transcript abundance and allele specificity of expression for five imprinted genes. Only 4% of clones recapitulated a blastocyst mode of expression for all five genes. Cloned embryos also exhibited extensive loss of allele-specific DNA methylation at the imprinting control regions of the H19 and Snprn genes. Thus, epigenetic errors arise very early in clonal development in the majority of embryos, indicating that reprogramming is inefficient and that some epigenetic information may be lost.
In Silico Modeling and Immunoinformatics Probing Disclose the Epitope Based PeptideVaccine Against Zika Virus Envelope Glycoprotein (2014)

Zika virus (ZIKV) is an aedes mosquito borne pathogen belonging to the member of flaviviridae subgroup is the causative agent of an emerging disease called Zika fever, known as a benign infection usually presenting as influenza like illness with cutaneous rash. Due to recent epidemic outbreaks it is realized as a major health risk which need enhanced surveillance, but no attempt has been made to design an epitope based peptide vaccine against Zika virus. Viral envelope proteins are derived from host cell membrane proteins with some viral glycoproteins and are used to cover their protective protein capsid, help the viruses to enter host cells and help them to avoid the host immune response. In this study, amino acid sequence of ZIKV envelope glycoprotein was obtained from a protein database and examined with in silico approaches to determine the most immunogenic epitopes for B cell and T cell which could induce humoral as well as cell mediated immune response. Both the linear and conformational epitopes for B cell were predicted by immunoinformatics tools housed in IEDB resources. The peptide sequence DAHAKRQTVVVLGSQEGAV from position 121 and peptide sequence from 117-137 amino acids were predicted as most potential B cell linear and conformational epitopes respectively. Epitopes for CD4+ and CD8+ T cell were also predicted by using tools within IEDB resource and peptide sequence MMLELDPPF from position 250-258 amino acids was predicted as most immunogenic CD8+ T cell epitope with immune response evoking ability prediction score (I pMHC) of 0.09139 and conservancy of 52.17%. The innate immune response for ZIKV envelope glycoprotein was determined by interferon (IFN)-gamma effectuation and mimicking capacity by immunoinformatics and molecular docking study respectively. However, this is an introductory approach to design an epitope based peptide vaccine against Zika virus; we hope this model will be very much helpful in designing and predicting novel vaccine candidate.
Image restoration using online photo collections (2009)

We present an image restoration method that leverages a large database of images gathered from the web. Given an input image, we execute an efficient visual search to find the closest images in the database; these images define the input's visual context. We use the visual context as an image-specific prior and show its value in a variety of image restoration operations, including white balance correction, exposure correction, and contrast enhancement. We evaluate our approach using a database of 1 million images downloaded from Flickr and demonstrate the effect of database size on performance. Our results show that priors based on the visual context consistently out-perform generic or even domain-specific priors for these operations.
A prospective surveillance model for physical rehabilitation of women with breast cancer (2012)

Chemotherapy-induced peripheral neuropathy (CIPN) results from damage to or dysfunction of the peripheral nerves. The development of CIPN is anticipated for the majority of breast cancer patients who receive neurotoxic chemotherapy, depending on the agent used, dose, and schedule. Sensory symptoms often predominate and include numbness, tingling, and distal extremity pain. Weakness, gait impairment, loss of functional abilities, and other deficits may develop with more severe CIPN. This article outlines a prospective surveillance model for physical rehabilitation of women with breast cancer who develop CIPN. Rehabilitative efforts for CIPN start at the time of breast cancer diagnosis and treatment planning. The prechemotherapy evaluation identifies patients with preexisting peripheral nervous system disorders that may place them at higher risk for the development of CIPN. This clinical evaluation should include a history focusing on symptoms and functional activities as well as a physical examination that objectively assesses the patient's strength, sensation, reflexes, and gait. Ongoing surveillance following the initiation of a neurotoxic agent is important to monitor for the development and progression of symptoms associated with CIPN, and to ensure its resolution over the long term. CIPN is managed best by a multidisciplinary team approach. Early identification of symptoms will ensure appropriate referral and timely symptom management. The prospective surveillance model promotes a patient-centered approach to care, from pretreatment through survivorship and palliative care. In this way, the model offers promise in addressing and minimizing both the acute and long-term morbidity associated with CIPN.
Fraxel Skin Resurfacing (2007)

Fractional photothermolysis is a new skin resurfacing laser technology for treating wrinkles, melanocytic pigmentation, scars, and photodamaged skin. Treatment with the Fraxel laser (Reliant Technologies, Inc.) creates microzones of injury in the skin that are surrounded by normal intervening skin that rapidly heals the injured tissue. From June to November of 2005, 70 patients underwent 2 to 6 treatments with the Fraxel laser (Reliant Technologies, Inc.) on the face and/or extremities for abnormal pigmentation, wrinkles, and scars. Treatments were 1 to 3 weeks apart. Clinically, the patient experienced little downtime other than erythema and edema for a few days followed by light skin exfoliation for a few days. After treatment, skin color and texture were more homogeneous with a decrease in the unwanted melanocytic pigmentation. The skin showed a decrease in rhytids. In summary, fractional photothermolysis improved skin color and texture and decreased fine wrinkles and melanocytic pigmentation with minimal downtime for the patient.
Switching Between OSTBC and Spatial Multiplexing with Linear Receivers in Spatially Correlated MIMO Channels (2006)

We present a low complexity adaptive transmission approach for spatially correlated MIMO channels. The proposed scheme adaptively switches between orthogonal space-time block codes (OSTBC) and spatial multiplexing (SM), depending of the channel correlation and SNR. We derive an exact closed-form expression and tight upper bound on the OSTBC capacity in double-correlated channels, and examine the relative capacity of OSTBC and SM in terms of the spatial correlation. We then derive efficient closed-form BER expressions for practical OSTBC transmission employing bit-interleaved coded modulation (BICM). Based on these results, we propose a practical adaptive algorithm which selects the combination of MIMO transmission scheme (OSTBC or SM), and BICM mode, which achieves the highest spectral efficiency whilst satisfying a pre-defined BER
Aerosol Administration of a Recombinant Adenovirus Expressing CFTR to Cystic Fibrosis Patients: A Phase I Clinical Trial (1997)

Ad CFTR, a replication-deficient adenovirus expressing the human cystic fibrosis transmembrane conductance regulator (CFTR), was administered by aerosolization in a single escalating dose to three pairs (cohorts) of cystic fibrosis (CF) patients. Buffer only was administered to the nose and lungs 9-14 days before nasal instillation of virus followed the day after by aerosolization of Ad CFTR to the lung. Nasal doses (defined in terms of viral plaque forming units, pfu) were 10(5), 10(7), and 4 x 10(8), whereas aerosolized doses were 10(7), 10(8), 5.4 x 10(8) for each cohort, respectively. No acute toxic effects were observed in the first 4 weeks after virus treatment. Shedding of infectious Ad CFTR was never detected, whereas detection of vector DNA sequences and CFTR expression demonstrated DNA transfer to the nose and airways of patients. No significant deviations in immunological and inflammatory parameters were observed in serum and in bronchoalveolar lavage (BAL). Importantly, for all patients, the serum anti-adenovirus antibody levels did not change significantly from baseline and no antibodies against adenovirus were found in BAL.
Unsupervised Monocular Depth Estimation with Left-Right Consistency (2017)

Learning based methods have shown very promising results for the task of depth estimation in single images. However, most existing approaches treat depth prediction as a supervised regression problem and as a result, require vast quantities of corresponding ground truth depth data for training. Just recording quality depth data in a range of environments is a challenging problem. In this paper, we innovate beyond existing approaches, replacing the use of explicit depth data during training with easier-to-obtain binocular stereo footage. We propose a novel training objective that enables our convolutional neural network to learn to perform single image depth estimation, despite the absence of ground truth depth data. Ex-ploiting epipolar geometry constraints, we generate disparity images by training our network with an image reconstruction loss. We show that solving for image reconstruction alone results in poor quality depth images. To overcome this problem, we propose a novel training loss that enforces consistency between the disparities produced relative to both the left and right images, leading to improved performance and robustness compared to existing approaches. Our method produces state of the art results for monocular depth estimation on the KITTI driving dataset, even outperforming supervised methods that have been trained with ground truth depth.
Chemotherapy use in stage III colon cancer: a National Cancer Database analysis (2015)

More than one-third did not receive adjuvant chemotherapy, although its use has increased in more recent years. Age was one of the most important determinants of chemotherapy use, which may explain higher rates in nonwhite and uninsured. In addition to patient characteristics, race, gender and socioeconomic factors influence chemotherapy use. These findings have important implications for healthcare reform.
Rice ( Oryza sativa ) centromeric regions consist of complex DNA (1998)

Rice bacterial artificial chromosome clones containing centromeric DNA were isolated by using a DNA sequence (pSau3A9) that is present in the centromeres of Gramineae species. Seven distinct repetitive DNA elements were isolated from a 75-kilobase rice bacterial artificial chromosome clone. All seven DNA elements are present in every rice centromere as demonstrated by fluorescence in situ hybridization. Six of the elements are middle repetitive, and their copy numbers range from approximately 50 to approximately 300 in the rice genome. Five of these six middle repetitive DNA elements are present in all of the Gramineae species, and the other element is detected only in species within the Bambusoideae subfamily of Gramineae. All six middle repetitive DNA elements are dispersed in the centromeric regions. The seventh element, the RCS2 family, is a tandem repeat of a 168-bp sequence that is represented approximately 6,000 times in the rice genome and is detected only in Oryza species. Fiber-fluorescence in situ hybridization analysis revealed that the RCS2 family is organized into long uninterrupted arrays and resembles previously reported tandem repeats located in the centromeres of human and Arabidopsis thaliana chromosomes. We characterized a large DNA fragment derived from a plant centromere and demonstrated that rice centromeres consist of complex DNA, including both highly and middle repetitive DNA sequences.
Global, regional, and national age–sex specific all-cause and cause-specific mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013 (2020)

Up-to-date evidence on levels and trends for age-sex-specific all-cause and cause-specific mortality is essential for the formation of global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013) we estimated yearly deaths for 188 countries between 1990, and 2013. We used the results to assess whether there is epidemiological convergence across countries.
EFFECT OF INCREASED INTRA-ABDOMINAL PRESSURE ON HEPATIC ARTERIAL, PORTAL VENOUS, AND HEPATIC MICROCIRCULATORY BLOOD FLOW (1992)

The effects of increased intra-abdominal pressure (IAP) on hepatic perfusion were studied in five anesthetized pigs. Doppler flow probes were used to measure hepatic artery blood flow (HABF) and portal venous blood flow (PVBF), and laser Doppler flowmetry was used to assess changes in hepatic microvascular blood flow (HMVBF). Hepatic blood flow responses to 10, 20, 30 and 40 mm Hg increases in IAP were assessed while the mean arterial BP (MAP) was maintained at baseline levels with IV crystalloid infusions. Although cardiac output and MAP were normal, HABF and HMVBF fell significantly with 10 mm IAP, and at 20 mm Hg IAP, HABF was 45% of the control value, PVBF was 65% of the control value, and HMVBF was 71% of the control value (p less than 0.05). At 30 and 40 mm Hg, hepatic blood flow was reduced even more. Thus, modest increases in IAP can cause significant impairment of hepatic perfusion despite a normal BP and cardiac output.
Completion of mammalian lagging strand DNA replication using purified proteins (1993)

We have modeled the reactions involved in the completion of lagging strand DNA replication using a synthetic DNA substrate and purified enzymes from calf thymus. We have demonstrated that each polymerase, alpha, delta, and epsilon, is capable of extending an upstream 3' terminus to generate a nick in the DNA substrate that is subsequently ligated by DNA ligase I. Synthesis by each polymerase and subsequent ligation occurred efficiently after the addition of the 50-kDa 5'- to 3'-exonuclease. Analyses are presented which show that a substantial proportion of the ligated products is the result of polymerase epsilon, exonuclease, and DNA ligase I, all acting on the same DNA template. That is, polymerase fills in the gap, then both the polymerase and exonuclease act, one adding and the other removing nucleotides, followed by ligation. Results presented suggest that polymerase alpha, delta, or epsilon may functionally interact with DNA ligase I and the 5'- to 3'-exonuclease to perform the enzymatic reactions required for the completion of lagging strand DNA synthesis.
Desensitization of G protein-coupled receptors. (1996)

Waning responsiveness to continuous or repeated stimulation constitutes the phenomenon of desensitization, which pervades biological systems. Over the last several years, molecular mechanisms for desensitization of cellular signaling through G protein-coupled receptors have been delineated, particularly at the level of the receptors themselves. This review focuses on those aspects of G protein-coupled receptor desensitization which occur within minutes of agonist exposure. Agonist-dependent desensitization of these receptors can reduce their signaling responsiveness to maximum stimulation by up to 70-80%; indeed, in some receptor systems, the process of receptor desensitization appears to effect the termination of the cellular signaling response. Agonist-induced desensitization involves phosphorylation of G protein-coupled receptors by two currently recognized classes of serine/threonine protein kinases. Second messenger-dependent kinases, phosphorylating a variety of proteins, mediate a generalized cellular hyporesponsiveness termed heterologous desensitization. G protein-coupled receptor kinases (GRKs) phosphorylate specifically agonist-occupied, or activated, receptors, and thereby initiate receptor-specific, or homologous, desensitization. GRK-mediated receptor phosphorylation facilitates the binding of an inhibitory arrestin protein to the phosphorylated receptor, an event which substantially impairs receptor signaling. The GRK family comprises six, and the arrestin family comprises four known members. Each GRK demonstrates the ability to phosphorylate a limited number of model receptor substrates, but the widespread expression of several GRKs and the two somatic arrestins suggest that GRK-initiated homologous desensitization is of general importance to a wide range of G protein-coupled receptors. Exploration of the substrate specificity for GRKs and the ligand specificity for arrestins remains in its early stages. Currently, GRKs can most readily be differentiated by the mechanisms each employs to associate with the plasma membrane. Accumulating data from human disease states and transgenic mice attest to the physiologic significance of GRK-initiated receptor desensitization.
Crystal Structure of the Heme-IsdC Complex, the Central Conduit of the Isd Iron/Heme Uptake System in Staphylococcus aureus (2007)

Pathogens such as Staphylococcus aureus require iron to survive and have evolved specialized proteins to steal heme from their host. IsdC is the central conduit of the Isd (iron-regulated surface determinant) multicomponent heme uptake machinery; staphylococcal cell-surface proteins such as IsdA, IsdB, and IsdH are thought to funnel their molecular cargo to IsdC, which then mediates the transfer of the iron-containing nutrient to the membrane translocation system IsdDEF. The structure of the heme-IsdC complex reveals a novel heme site within an immunoglobulin-like domain and sheds light on its binding mechanism. The folding topology is reminiscent of the architecture of cytochrome f, cellobiose dehydrogenase, and ethylbenzene dehydrogenase; in these three proteins, the heme is bound in an equivalent position, but interestingly, IsdC features a distinct binding pocket with the ligand located next to the hydrophobic core of the beta-sandwich. The iron is coordinated with a tyrosine surrounded by several non-polar side chains that cluster into a tightly packed proximal side. On the other hand, the distal side is relatively exposed with a short helical peptide segment that acts as a lip clasping onto almost half of the porphyrin plane. This structural feature is argued to play a role in the mechanism of binding and release by switching to an open conformation and thus loosening the interactions holding the heme. The structure of the heme-IsdC complex provides a template for the understanding of other proteins, such as IsdA, IsdB, and IsdH, that contain the same heme-binding module as IsdC, known as the NEAT (near transporter) domain.
[Chemical composition and cryoprotective activity of ethanol extract from winter caterpillars Aporia crataegi L]. (2004)

Glycerol, alpha-carotene, and other yet unidentified compounds have been found in the ethanol extract from winter caterpillars of the black-veined white (Aporia crataegi L.). We have shown that the ethanol extract has a cryoprotective effect on human peripheral blood lymphocytes, and this activity is approximately three times higher than that of glycerol (particularly, in the case of repeated freezing), which is one of the best cryoprotectors.
Lymphokines (1987)

LYMPHOKINES are polypeptide products of activated lymphocytes that participate in a variety of cellular responses, including the regulation of the immune system. They are released in response to antigen, but in contrast to the chemical composition of antibodies, their chemical composition is not determined by that of the stimulating antigen. Lymphokines were originally thought to be produced only by lymphocytes and to communicate with other cells of the immune system. It is now clear that neither the production of lymphokines nor their effects are restricted to lymphoid cells. For these reasons, the term "lymphokine" is yielding to the more general . . .