gebhart/patrepeval huggingface dataset:
The Crystallographic Structure of the B800-820 LH3 Light-Harvesting Complex from the Purple Bacteria Rhodopseudomonas Acidophila Strain 7050 (2001)

The B800-820, or LH3, complex is a spectroscopic variant of the B800-850 LH2 peripheral light-harvesting complex. LH3 is synthesized by some species and strains of purple bacteria when growing under what are generally classed as "stressed" conditions, such as low intensity illumination and/or low temperature (<30 degrees C). The apoproteins in these complexes modify the absorption properties of the chromophores to ensure that the photosynthetic process is highly efficient. The crystal structure of the B800-820 light-harvesting complex, an integral membrane pigment-protein complex, from the purple bacteria Rhodopseudomonas (Rps.) acidophila strain 7050 has been determined to a resolution of 3.0 A by molecular replacement. The overall structure of the LH3 complex is analogous to that of the LH2 complex from Rps. acidophila strain 10050. LH3 has a nonameric quaternary structure where two concentric cylinders of alpha-helices enclose the pigment molecules bacteriochlorophyll a and carotenoid. The observed spectroscopic differences between LH2 and LH3 can be attributed to differences in the primary structure of the apoproteins. There are changes in hydrogen bonding patterns between the coupled Bchla molecules and the protein that have an effect on the conformation of the C3-acetyl groups of the B820 molecules. The structure of LH3 shows the important role that the protein plays in modulating the characteristics of the light-harvesting system and indicates the mechanisms by which the absorption properties of the complex are altered to produce a more efficient light-harvesting component.
An integration platform for heterogeneous sensor systems in GITEWS – Tsunami Service Bus (2010)

Abstract. The German Indonesian Tsunami Early Warning System (GITEWS) is built upon a complex sensor data infrastructure. To best fulfill the demand for a long living system, the underlying software and hardware architecture of GITEWS must be prepared for future modifications both of single sensors and entire sensors systems. The foundation for a flexible integration and for stable interfaces is a result of following the paradigm of a Service Oriented Architecture (SOA). The Tsunami Service Bus (TSB) – our integration platform in GITEWS – realizes this SOA approach by implementing the Sensor Web Enablement (SWE) standards and services. This paper focuses on architectural and implementation aspects of the TSB. Initially, the general architectural approach in GITEWS by SOA and SWE is presented. Based on this conception, the concrete system architecture of GITEWS is introduced. The sensor integration platform TSB is then discussed in detail, following by its primary responsibilities and components. Special emphasis is laid on architectural transparency, comprehensible design decisions, and references to the applied technology.
A Possible Mechanism of Direct Injury to the EPL Tendon at Lister’s Tubercle During Falls with the Wrist Fully Extended (2008)

We present three cases of pathology of the extensor pollicis longus tendon at the level of Lister's tubercle after falls with the wrist fully extended. A small anatomical study demonstrates the possibility of the base of the third metacarpal impacting this area in hyperextension. This mechanism of injury to the tendon may explain the clinical findings.
Numerical Simulation of Third-Generation HgCdTe Detector Pixel Arrays (2013)

In this paper, we present a physics-based full 3-D numerical simulation model of third-generation infrared (IR) detector pixel arrays. The approach avoids geometrical simplifications typical of 1-D and 2-D models that can introduce errors which are difficult to quantify. We have used a finite-difference time-domain technique to compute the optical characteristics including the reflectance and the carrier generation rate in the device. Subsequently, we employ the finite-element method to solve the drift-diffusion equations on a mixed-element grid to compute the electrical characteristics including the I(V) characteristics and quantum efficiency. Furthermore, we have used this model to study HgCdTe two-color detectors that operate in the medium-wave to long-wave IR and photovoltaic pixel arrays employing a photon-trapping structure realized with a periodic array of pillars that operate in the medium-wave IR.
Introduction (2016)

Journal of NeuroendocrinologyVolume 28, Issue 7 Editorial Introduction Shaila K. Mani, Shaila K. Mani smani@bcm.edu Departments of Molecular and Cellular Biology and Neuroscience, Baylor College of Medicine, Houston, TX, USASearch for more papers by this author Shaila K. Mani, Shaila K. Mani smani@bcm.edu Departments of Molecular and Cellular Biology and Neuroscience, Baylor College of Medicine, Houston, TX, USASearch for more papers by this author First published: 24 June 2016 https://doi.org/10.1111/jne.12406Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume28, Issue7Special Issue: Reviews from the International Workshop in Neuroendocrinology (2015): Steroid hormones: Mechanisms and FunctionsJuly 2016 RelatedInformation
Generalizable convolutional neural network (CNN) classification of breast cancer using images from two optical coherence tomography (OCT) systems (2021)

The purpose of this study was to develop a generalizable convolutional neural network (CNN) classification technique of optical coherence tomography (OCT) images of breast tissue acquired from multiple OCT systems. We imaged lumpectomy and mastectomy specimens (acquired through the Columbia University Tissue Bank) from 31 patients. In our early results, we classified the images into healthy tissue (adipose and stroma) and diseased, which included ductal carcinoma in situ (DCIS), mucinous carcinoma, and invasive ductal carcinoma (IDC). Our goal is to expand our classification to differentiate the diseased tissue into subclasses of DCIS, IDC, mucinous carcinoma, and benign tissue.
A highly efficient synthetic procedure for deuteriating imidazoles and imidazolium salts (2001)

Both substituted imidazoles and 1,3-dialkylimidazolium salts can be fully deuteriated on the heterocyclic ring using D2O over heterogeneous Pd catalysts: deuteriated 1-alkyl-3-methylimidazolium chloride and hexafluorophosphate ionic liquids can also be prepared in good yields utilising readily available and relatively low cost sources of deuterium.
Selective Inhibitors of Glutathione Transferase P1 with Trioxane Structure as Anticancer Agents (2015)

The response to chemotherapy in cancer patients is frequently compromised by drug resistance. Although chemoresistance is a multifactorial phenomenon, many studies have demonstrated that altered drug metabolism through the expression of phase II conjugating enzymes, including glutathione transferases (GSTs), in tumor cells can be directly correlated with resistance against a wide range of marketed anticancer drugs. In particular, overexpression of glutathione transferase P1 (GSTP1) appears to be a factor for poor prognosis during cancer therapy. Former and ongoing clinical trials have confirmed GSTP1 inhibition as a principle for antitumor therapy. A new series of 1,2,4-trioxane GSTP1 inhibitors were designed via a type II photooxygenation route of allylic alcohols followed by acid-catalyzed peroxyacetalization with aldehydes. A set of novel inhibitors exhibit low micromolar to high nanomolar inhibition of GSTP1, revealing preliminary SAR for further lead optimization. Importantly, high selectivity over another two human GST classes (GSTA1 and GSTM2) has been achieved. The trioxane GSTP1 inhibitors may therefore serve as a basis for the development of novel drug candidates in overcoming chemoresistance.
Synthesis and Calcium Channel Antagonist Activity of Dialkyl 1,4-Dihydro-2,6-dimethyl-4-[4-(1-methoxycarbonyl-1,4-dihydropyridyl)]-3,5- pyridinedicarboxylates (1999)

A novel class of dialkyl 1,4-dihydro-2,6-dimethyl-4-[4-(1- methoxycarbonyl-1,4-dihydropyridyl)]-3,5-pyridinedicarboxylates (8-14) were synthesized and evaluated as calcium channel antagonists. The differences in activity among members of this new class of compounds was less than one log unit (IC50 range of 1.12 x 10(-6) to 8.57 x 10(-6) M), relative to the reference drug nifedipine (IC50 = 1.43 x 10(-8) M). The small differences in potency, irrespective of the size of the dialkyl (Me, Et, i-Pr, i-Bu) ester substituents, is attributed to the fact that the N-CO2Me substituent is too far removed from the C-3 and C-5 ester substituents to undergo non-bonded steric interactions. The 4-[4-(1-methoxycarbonyl-1,4-dihydropyridyl) moiety in this new class of compounds is bioisosteric with a C-4 4-nitrophenyl, or a 4-pyridyl, substituent in classical 1,4-dihydropyridines.
HeteroGen: Automatic Synthesis of Heterogeneous Cache Coherence Protocols (2023)

We address the two challenges architects face when designing heterogeneous processors with cache-coherent shared memory. First, we introduce HeteroGen, an automated tool for composing clusters of cores, each with its own coherence protocol. Second, we show that the output of HeteroGen conforms to a precisely defined memory consistency model that we call a compound consistency model. We also demonstrate that HeteroGen can correctly fuse a wide range of coherence protocols. Our experiments indicate that protocols generated by HeteroGen perform comparably to a publicly available manually generated heterogeneous protocol.
The Sepsis-Coagulant Axis: A Review (1998)

Activation of coagulation is a normal component of the acute inflammatory response. Inflammatory cytokines initiate coagulation events locally at sites of inflammation by converting endothelium from an antithrombotic surface to a prothrombotic surface; by stimulating tissue factor production, which activates both the extrinsic and intrinsic coagulation systems; and by stimulating production of platelet-activating factors. The fibrinolytic system is initially activated but is subsequently inhibited. This results in a marked imbalance in coagulation and fibrinolysis resulting in a net procoagulant state. When thrombin generation and platelet activation exceed the body's capacity to inactivate or remove these factors, disseminated intravascular coagulation (DIC) results. DIC directly contributes to multiple organ failure and death associated with sepsis. Presently available treatments (i.e., heparin and aspirin) are relatively ineffective in treating DIC; however, newer, more potent drugs may soon be available for clinical use.
INF-γ encoding plasmid administration triggers bone loss and disrupts bone marrow microenvironment (2016)

IFN-γ is a pleotropic cytokine produced in the bone microenvironment. Although IFN-γ is known to play a critical role on bone remodeling, its function is not fully elucidated. Consistently, outcomes on the effects of IFN-γ recombinant protein on bone loss are contradictory among reports. In our work we explored, for the first time, the role of IFN-γ encoding plasmid (pIFN-γ) in a mouse model of osteopenia induced by ovariectomy and in the sham-operated counterpart to estimate its effects in skeletal homeostasis. Ovariectomy produced a dramatic decrease of bone mineral density (BMD). pINF-γ injected mice showed a pathologic bone and bone marrow phenotype; the disrupted cortical and trabecular bone microarchitecture was accompanied by an increased release of pro-inflammatory cytokine by bone marrow cells. Moreover, mesenchymal stem cells' (MSCs) commitment to osteoblast was found impaired, as evidenced by the decline of osterix-positive (Osx<sup>+</sup>) cells within the mid-diaphyseal area of femurs. For instance, a reduction and redistribution of CXCL12 cells have been found, in accordance with bone marrow morphological alterations. As similar effects were observed both in sham-operated and in ovariectomized mice, our studies proved that an increased IFN-γ synthesis in bone marrow might be sufficient to induce inflammatory and catabolic responses even in the absence of pathologic predisposing substrates. In addition, the obtained data might raise questions about pIFN-γ's safety when it is used as vaccine adjuvant.
U-Shape Slots Structure on Substrate Integrated Waveguide for 40-GHz Bandpass Filter Using LTCC Technology (2014)

Millimeter-wave (mmW) bandpass filter using substrate integrated waveguide (SIW) is proposed in this paper. The propagation constants of three different types of electromagnetic bandgap (EBG) units are discussed and compared with their passbands and stopbands performance. The slotted-SIW unit shows a very good lower stopband and upper stopband performance. The mmW bandpass filter with three cascaded uniform slotted-SIW-based EBG units is constructed and designed at 40 GHz. The extracted coupling coefficient (K) and quality factor (Q) are used to determine the filter circuit dimensions. To prove the validity, the previous proposed structure is fabricated in a single circuit layer using low-temperature co-fired ceramic technology and measured at 40 GHz, respectively. The measured results are in good agreement with simulated results in such frequency and the measured insertion losses at 40 GHz is 1.42 dB, respectively.
Six Homologs and One Active Gene Copy (1998)

The 12 locus in tomato confers resistance to race 2 of the soil-borne fungus Fusarium oxysporum f sp lycopersici. The selective restriction fragment amplification (AFLP) positional cloning strategy was used to identify 12 in the tomato ge? nome. A yeast artificial chromosome (YAC) clone covering ^750 kb encompassing the 12 locus was isolated, and the AFLP technique was used to derive tightly linked AFLP markers from this YAC clone. Genetic complementation analy? sis in transgenic R1 plants using a set of overlapping cosmids covering the 12 locus revealed three cosmids giving full resistance to F. o. lycopersici race 2. These cosmids shared a 7-kb DNA fragment containing an open reading frame en? coding a protein with similarity to the nucleotide binding site leucine-rich repeat family of resistance genes. At the 12 locus, we identified six additional homologs that included the recently identified I2C-1 and I2C-2 genes. However, cosmids containing the I2C-1 or I2C-2 gene could not confer resistance to plants, indicating that these members are not the functional resistance genes. Alignments between the various members of the 12 gene family revealed two sig? nificant variable regions within the leucine-rich repeat region. They consisted of deletions or duplications of one or more leucine-rich repeats. We propose that one or both of these leucine-rich repeats are involved in Fusarium wilt re? sistance with 12 specificity.
Data packets scheduling and encoding method for multicast automatic repeat request communication system, involves transmitting one of composite data packets to two receivers by sender. (2006)

NOVELTY - The method involves obtaining feedback information from two receivers indicating received data packets, and forming a composite data packet as a weighted linear combination of regular data packets. Coding weights of a weight vector are adapted based on the feedback information for each of the composite data packet, such that the composite packet represents a linear combination of the regular packets for the receivers of the data packet previously received by the receivers during a multicast session. One of the composite data packets is transmitted to the receivers by a sender. USE - Method for scheduling and encoding data packets for transmission in a multicast session from a sender to two receivers in a multicast automatic repeat request (ARQ) communication system. Can also be used in a cellular system with a base station in communication with a set of mobile terminals. ADVANTAGE - The method effectively schedules and encodes the data packets for transmission in the multicast session from the sender to the receivers in the multicast automatic repeat request (ARQ) communication system. The method enables improved throughput efficiency for the reliable multicast, and provides deterministically decodable re-transmission scheme. The method provides highly throughput-efficient strategy for reliable multicasting. The method efficiently provides the multicast strategy that enables enhanced throughput, reduced delay and/or reduced energy consumption. DETAILED DESCRIPTION - An INDEPENDENT CLAIM is also included for a sender for use in a multicast automatic repeat request (ARQ) communication system, comprising an arrangement for scheduling and encoding data packets for transmission in a multicast session from the sender to two receivers. DESCRIPTION OF DRAWING(S) - The drawing shows a schematic flow diagram of a method for scheduling and encoding regular data packets into a composite data packet.
A Clinician-Driven Automated System for Integration of Pharmacogenetic Interpretations Into an Electronic Medical Record (2012)

Advances in pharmacogenetic testing will expand the number of clinically important pharmacogenetic variants. Communication and interpretation of these test results are critical steps in implementation of pharmacogenetics into the clinic. Computational tools that integrate directly into the electronic medical record (EMR) are needed to translate the growing number of genetic variants into interpretive consultations to facilitate gene-based drug prescribing. Herein, we describe processes for incorporating pharmacogenetic tests and interpretations into the EMR for clinical practice. Clinical Pharmacology & Therapeutics (2012); 92 5, 563–566. doi:10.1038/clpt.2012.140
Design of a Phase 3 Trial to Evaluate the Long-Term Efficacy and Safety of Ataluren in Patients with Nonsense Mutation Duchenne Muscular Dystrophy (P2.329) (2018)

Present the study design of a phase 3 randomized, double-blind, placebo-controlled trial with an open-label extension period designed to evaluate the long-term efficacy and safety of ataluren in boys with nmDMD (Study 041).
A STUDY ON FUZZY CONTROL OF BULLDOZER BLADE (1992)

建設施工の自動化に向けて押土作業時のブレードへのファジィ制御の適用を試みた. ファジィ制御における非ファジィ化の方法, ラベル数など種々の制御条件が結果に与える影響をシミュレーションおよび室内モデル試験により明らかにした. 特にファジィ制御を開始し始める最小値の設定については, 地盤条件を考慮した適切な制御条件が選択されることにより押土能率を向上できることが明らかになった.
Abstract 3412: Viscous Dissipation Power Loss of the Total Cavopulmonary Connection Evaluated Using Phase Contrast Magnetic Resonance Imaging (2006)

Introduction: Two variations of the total cavopulmonary connection (TCPC) used to correct single ventricle physiology are the intra-atrial (IA) and the extra-cardiac (EC) connections. There is no c...
Deployment of CCTV in Saudi Arabia: Security, Culture and Religion (2015)

Deployment of CCTV surveillance systems has now become a worldwide practice for securing people and businesses alike. A common goal of all CCTV surveillance systems is to detect crime and disorder in a timely manner, enabling the law enforcers to possibly prevent it from happening. The effective deployment of CCTV in Saudi Arabia is of particular interest to researchers and decision-makers as in addition to the usual cons and pros, cultural and religious factors do severely hinder its effective implementation. In particular, as prescribed in the sharia law, men or women are not allowed to take picture/video or acquire picture/video; hence making it very hard to argue in favour of the case for CCTV systems. Based on a simple model of cost-benefit analysis, this study attempts to evaluate the social costs and returns associated with the deployment of CCTV surveillance systems in both public and private places across the country. In so doing, the research has focused on a case study of a large public hospital in Riyadh as a pilot case for evaluation of effectiveness of use of CCTV. Using a large sample of doctors, nurses, workers and patients of the hospital, the study has produced a structured questionnaire survey. The preliminary findings are indicative of several main issues. Firstly, due to lack of education on the part of some patients and workers, over 52% of such participants declared that they had no knowledge about the potential usefulness of the CCTV surveillance in crime reduction. Secondly, a significantly large number of doctors and nurses declared that they were fully supportive of the surveillance systems as they believed it would help reduce theft and provide a safe and secure environment for them to work. Thirdly, although over 50% of participants tend to believe that CCTV systems can help reduce crimes, they were concerned that the staff in charge of such CCTV systems may abuse the power and hence jeopardise the true effectiveness of the system. Finally, according to the initial findings of the study, it is anticipated that there would be more CCTV systems in place in Saudi Arabia as the issue of security tends to overshadow other cultural and religious issues.
Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice (2020)

Protamines are the safeguards of the paternal sperm genome. They replace most of the histones during spermiogenesis, resulting in DNA hypercondensation, thereby protecting its genome from environmental noxa. Impaired protamination has been linked to male infertility in mice and humans in many studies. Apart from impaired DNA integrity, protamine-deficient human and murine sperm show multiple secondary effects, including decreased motility and aberrant head morphology. In this study, we use a Protamine<i>-2</i> (<i>Prm2</i>)-deficient mouse model in combination with label-free quantitative proteomics to decipher the underlying molecular processes of these effects. We show that loss of the sperm's antioxidant capacity, indicated by downregulation of key proteins like Superoxide dismutase type 1 (SOD1) and Peroxiredoxin 5 (PRDX5), ultimately initiates an oxidative stress-mediated destruction cascade during epididymal sperm maturation. This is confirmed by an increased level of 8-OHdG in epididymal sperm, a biomarker for oxidative stress-mediated DNA damage. <i>Prm2</i>-deficient testicular sperm are not affected and initiate the proper development of blastocyst stage preimplantation embryos in vitro upon intracytoplasmic sperm injection (ICSI) into oocytes. Our results provide new insight into the role of <i>Prm2</i> and its downstream molecular effects on sperm function and present an important contribution to the investigation of new treatment regimens for infertile men with impaired protamination.
Sparse Data Acquisition on Emerging Memory Architectures (2018)

Emerging memory devices, such as resistive crossbars, have the capacity to store large amounts of data in a single array. Acquiring the data stored in large-capacity crossbars in a sequential fashion can become a bottleneck. We present practical methods, based on sparse sampling, to quickly acquire sparse data stored on emerging memory devices that support the basic summation kernel, reducing the acquisition time from linear to sub-linear. Experimental results show that at least an order of magnitude improvement in acquisition time can be achieved when the data is sparse.
Clusterin Decreases Oxidative Stress in Lung Fibroblasts Exposed to Cigarette Smoke (2006)

We conclude that clusterin may have a protective effect against cigarette smoke-induced oxidative stress in lung fibroblasts.