gebhart/patrepeval huggingface dataset:
Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum (2020)

A novel anaerobic, endospore-forming bacterium (strain M08 DMB<sup>T</sup>) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells of the strain were motile rods 1.3-2.0 µm long and 0.4 µm in diameter. The temperature range for growth was 5-42 °C, with an optimum at 30 °C. The pH range for growth was H 6.5-11.0, with an optimum at pH 8.0. Growth of strain M08 DMB<sup>T</sup> was observed at NaCl concentrations of 0-5.0 % (w/v) with an optimum at 1.0 %. Strain M08 DMB<sup>T</sup> utilized 3,4-dimethoxybenzoic acid, 2-methoxyphenol, carbon monoxide, glucose, fructose, mannose, xylose and yeast extract. The end product of glucose fermentation was acetate. The DNA G+C content of strain M08 DMB<sup>T</sup> was 32.3 mol% (obtained via whole genome sequencing). The closest phylogenetic relative of strain M08 DMB<sup>T</sup> was <i>Alkalibaculum bacchi</i> (family <i>Eubacteriaceae</i>, class <i>Clostridia</i>) with 95.17 % 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08 DMB<sup>T</sup> is considered to represent a novel species of the genus <i>Alkalibaculum</i>, for which the name <i>Alkalibaculum sporogenes</i> sp. nov. is proposed. The type strain of <i>Alkalibaculum sporogenes</i> is M08 DMB<sup>T</sup> (=KCTC 15840<sup>T</sup>=VKM B-3387<sup>T</sup>).
Insertion Polymerization of Cyclobutenes by Detouring Pericyclic Opening (2006)

In this communication, Seto and Novak cleverly designed insertion-polymerizable cyclobutenes. These molecules generally are difficult to polymerize in an insertion fashion since they isomerize to butadienes through pericyclic ring-opening reactions. By locking the cyclobutene with a cis-fused ring system, they were able to achieve fairly high-molecular-weight polymers (Mn is up to 155,000) after optimizing conditions.
Supplementary Table 3 from Cancer-Testis Genes Are Coordinately Expressed and Are Markers of Poor Outcome in Non–Small Cell Lung Cancer (2023)

&lt;p&gt;CT-X expression frequency and clinical characteristics&lt;/p&gt;
Retinal Microvascular Signs and 10-Year Risk of Cerebral Atrophy (2010)

Retinopathy and arteriovenous nicking are predictive of long-term risk of ventricular enlargement, but not of sulcal widening, independent of cardiovascular risk factors. These data support a microvascular etiology for subcortical but not cortical cerebral atrophy.
Pilot study of a new angiotensin II receptor antagonist, TCV-116: effects of a single oral dose on blood pressure in patients with essential hypertension. (1993)

After a 1-week placebo control period, six hypertensive patients (mean age, 67 years) each received single doses of 1, 2.5, and 5 mg of TCV-116 at 2- to 3- day intervals. Systolic and diastolic blood pressures were significantly lower after the final dose (5 mg) of TCV-116 than on the last day of the placebo period. Blood pressures were decreased after each dose of TCV-116 in a dose-dependent fashion from 2 hours after administration and reached a nadir at 4 to 6 hours. After 2.5 and 5 mg of TCV-116, the hypotensive effect was sustained for 24 hours. Pulse rate did not change significantly. Plasma renin activity and angiotensin I levels increased in a dose-dependent fashion after TCV-116, but the changes were not significant. No changes were noted in plasma aldosterone or angiotensin II levels. One patient reported mild light-headedness after 5 mg of TCV-116. No other side effects or abnormal laboratory tests results were noted. It appears that TCV-116 is a safe and effective antihypertensive agent.
Supplementary Figure 1 from A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition (2023)

&lt;p&gt;Supplementary Figure 1 PDF file - 375K, Primary melanocytes expressing oncogenic B-RAF are rendered resistant to PLX4720 following NF1 knockdown. (A) Immortalized human primary melanocytes expressing Myc-tagged B-RAFV600E were infected with shRNAs against NF1 and a control, non-targeting shRNA. Cells were treated with a 9-point concentration response of PLX4720 for 7 d and cell proliferation assessed by cell-titer glo assay. (B) Primary melanocytes from (A) were seeded at low density and exposed to 3 �M PLX4720. Colony formation was determined after 10 d in culture by staining with crystal violet. (C) Primary melanocytes infected with the indicated shRNAs were treated with 0.2 or 1 �M PLX4720 for 16 h. Cell lysates were analyzed for the indicated proteins.&lt;/p&gt;
A double coaxial delivery system for deployment of a two-stage stent-graft: An experimental feasibility study (2000)

The double coaxial delivery system enabled quick endovascular assembly of a two-stage aortic stent-graft.
DCC promoter hypermethylation in esophageal squamous cell carcinoma (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

35 

Deleted in Colorectal Cancer ( DCC ) is a putative tumor suppressor gene whose loss has been implicated in colorectal tumorigenesis. Decreased or loss of DCC expression has been demonstrated in a number of human cancers, including esophageal squamous cell carcinoma (ESCC). In this study, we analyzed ESCC cell lines and primary ESCCs as well as their corresponding normal tissues for DCC methylation by bisulfite sequencing and/or quantitative methylation-specific PCR (qMSP). When a qMSP cut-off value for positivity was set to 1.0, DCC methylation was detected in 10 of 12 ESCC cell lines tested, 74% of primary ESCCs (n=70), and 0% of corresponding normal esophageal tissues (n=20). DCC expression was undetectable in the majority of ESCC cell lines, and treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine reactivated gene expression. DCC overexpression suppressed colony formation in ESCC cell lines, suggesting that DCC may function as a tumor suppressor gene in the esophagus. We have demonstrated that DCC methylation is a frequent and cancer-specific event in primary ESCCs with 74% sensitivity and 100% specificity, suggesting that DCC and associated pathways may represent a new therapeutic target. Moreover, detection of DCC promoter methylation may potentially be used as a biomarker in the early detection of human ESCC.
Silicon-mediated annulation. Part 1. A synthesis of tetrahydropyran-4-ones, oxepan-4-ones, and oxocan-4-ones via intramolecular directed aldol reactions (1985)

A Lewis acid-catalysed intramolecular directed aldol condensation of enol silanes and acetals was used to prepare tetrahydropyran-4-ones, oxepan-4-ones, and oxocan-4-ones. The course of the cyclisations was influenced by the Lewis acid and the stereochemistry of the starting material.
Military-Specific Normative Data for Cognitive and Motor Single- and Dual-Task Assessments for Use in Mild Traumatic Brain Injury Assessment (2020)

Differences in cognitive performance and postural stability measures may be influenced by demographic differences between military and civilian cohorts. Thus, military-specific normative datasets must be established to optimize clinical interpretation of Cleveland Clinic Concussion assessments.
Cervical and systemic innate immunity predictors of HIV risk linked to genital herpes acquisition and time from HSV-2 seroconversion (2022)

Abstract Objectives To examine innate immunity predictors of HIV-1 acquisition as biomarkers of HSV-2 risk and biological basis for epidemiologically established HIV-1 predisposition in HSV-2 infected women. Methods We analyzed longitudinal samples from HIV-1 negative visits of 1019 women before and after HSV-2 acquisition. We measured cervical and serum biomarkers of inflammation and immune activation previously linked to HIV-1 risk. Protein levels were Box–Cox transformed and odds ratios for HSV-2 acquisition were calculated based on top quartile or below/above median levels for all HSV-2 negative visits. Bivariate analysis determined the likelihood of HSV-2 acquisition by biomarker levels preceding infection. Linear mixed-effects models evaluated if biomarkers differed by HSV-2 status defined as negative, incident, or established infections with an established infection cut-off starting at 6 months. Results In the cervical compartment, two biomarkers of HIV-1 risk (low SLPI and high BD-2) also predicted HSV-2 acquisition. In addition, HSV-2 acquisition was associated with IL-1β, IL-6, IL-8, MIP-3α, ICAM-1 and VEGF when below median levels. Systemic immunity predictors of HSV-2 acquisition were high sCD14 and IL-6, with highest odds when concomitantly increased (OR=2.23, 1.49-3.35). Concomitant systemic and mucosal predictors of HSV-2 acquisition risk included: 1) serum top quartile sCD14 with cervical low SLPI, VEGF and ICAM-1, or high BD-2; serum high IL-6 with cervical low VEGF and ICAM-1, SLPI, IL-1β and IL-6, and 3) serum low CRP with cervical high BD-2. Most cervical biomarkers were decreased after HSV-2 acquisition compared to the HSV-2 negative visits, with incident infections associated with a larger number of suppressed cervical biomarkers and lower serum IL-6 levels compared to established infections. Conclusions A combination of systemic immunoinflammatory and cervical immunosuppressed states predicts HSV-2 acquisition. A persistently suppressed innate immunity during incident infection may add to the increased HIV-1 susceptibility. Key Messages A combination of altered systemic and cervical immunity precedes and predicts risk of HSV-2 acquisition. Factors causing cervical mucosal imbalance (low SLPI and high BD-2) may predispose to both HIV-1 and HSV-2 acquisition In comparison to non-infected, HSV-2 infected women show suppressed cervical innate immunity Compared to women with established HSV-2 infection, those with incident infections within 6 months from seroconversion are more immunosuppressed both at the mucosal and peripheral level, adding to the biology of HIV predisposition.
Selective Probes for Nicotinic Acetylcholine Receptors from Substituted AE-Bicyclic Analogs of Methyllycaconitine (1998)

A concise, practical approach to substituted [3.3.1]-AE-bicyclic analogs of methyllycaconitine (MLA) has been developed employing dianion alkylation and double Mannich reactions. Acetylide anion addition to substituted cyclohexanones and manipulation of the acetylide alkoxide dianion generates useful bis-propargyl tertiary alcohols. The design and synthesis of probes for nicotinic acetylcholine receptors (nAChR) affords possible leads for pesticides. MLA also has potential in probing neuronal nAChR which are implicated in some mechanisms of neurodegeneration.
Standard and derived Planck quantities: Selected analysis and observations (2011)

We provide an overview of the fundamental units of physical quantities determined naturally by the values of fundamental constants of nature. We discuss a comparison between the “Planck units”, now widely used in theoretical physics, and the pre-quantum “Stoney units” in which, instead of the Planck constant, the charge of the electron is used with very similar quantitative results. We discuss some of the hindsight physical motivation for such units, and also put forth a summary of the arguments supporting various cases for making specific physical interpretations of the meanings of some of these units. The new aspects we discuss are a possible physical basis for the Stoney units, their link to the Planck units, and also the importance of Planck units for thermodynamical quantities in the context of quantum gravity.
Circuit and antenna-in-package innovations for scaled mmWave 5G phased array modules (2018)

Directional communication at millimeter-wave (mmWave) frequencies is one of the key technologies under development towards the anticipated deployment of fifth generation mobile access (5G). Silicon-based multi-antenna systems are strong candidates for the implementation of such directional links; however, the performance requirements are in general significantly more challenging than those posed by mmWave WLAN links demonstrated so far (e.g. for 802.11ad). This work presents an overview of recent innovations in circuit design, antenna design, and beamforming architecture which enable complex phased arrays with precise and agile beamforming for mmWave-based 5G communications. Specifically, this work discusses: (1) a 28-GHz phase shifting transceiver front end, (2) beamforming architecture considerations to enable dual polarized operation as well as multi beam configurability, and (3) two different 28-GHz antenna-in-package (AiP) designs. These advances have been jointly demonstrated in a 64-element dual polarized phased array antenna module (PAAM) consisting of four SiGe ICs and an AiP array. The PAAM supports two simultaneous and independent 64-element beams in either TX or RX modes. PAAM-level measurement results over the air without calibration show +/- 50° beam scanning with >10dB silde-lobe rejection, <;1.4° beam steering resolution with 0.6° RMS error, and 54 dBm saturated EIRP in each polarization. On-wafer measurement results from a front-end breakout and a full phased array IC are presented as well.
Prototype Evaluation of the 38GHz-band Lens Antenna for High Altitude Platform Station (HAPS) Ground Station System (2021)

At a time when expectations are high for the rapid realization of broadband communications using HAPS (High-Altitude Platform Station), which can secure redundant routes over the sky, international movement toward commercialization is accelerating, environmental improvement and technological development are advancing, and their popularization is expected to expand. On the other hand, it is necessary to develop a radio system capable of providing high-speed and high-capacity circuits by using the wide-band frequency of the millimeter wave band (Q/V band) using HAPS, and to realize the improvement of frequency utilization efficiency in the millimeter wave band and the practical application of HAPS system. For this purpose, it is necessary to establish a frequency sharing technology to reduce the effect of radio interference with terrestrial mobile communication systems and to realize efficient use of frequencies. In this paper, as one of the research and development of three dimensional non-terrestrial communication network (NTN) using HAPS, the research result of lens antenna of the 38 GHz band ground station antenna system for HAPS is shown.
Microbial Biotechnology: Scope, Techniques, Examples (2007)

One can be a good biologist without necessarily knowing much about microorganisms, but one cannot be a good microbiologist without a fair basic knowledge of biology!– Stanier, R. Y., Doudoroff, M., and Adelberg, E. A. (1957). The Microbial World. p. vii, Englewood Cliffs, NJ: Prentice-Hall, Inc.
Prediction of subcellular localizations using amino acid composition and order. (2001)

Subcellular localization is important for proteins to function. For the prediction of subcellular localizations, we have developed a method, SortPred, using the amino acid composition and order. The composition represents the global features, e.g., the amino acid composition in the full or partial sequences, while the order represents the local features, e.g., the amino acid sequence order. The former was represented by neural networks and the latter was represented by a hidden Markov model. This method predicted the signal peptides (SP), the mitochondrial targeting peptides (mTP), the chloroplast transit peptides (cTP), and the nuclear or cytosolic sequences (other) comparing together the previous methods, this method achieved slightly higher prediction accuracy, 86% for plant and 91% for non-plant. We analyzed the trained neural networks and hidden Markov models and found out that these models well represent the biological features of the sequences.
Tailoring the Pore Alignment for Rapid Ion Transport in Microporous Carbons (2010)

The power density and charge-discharge time of electrical double layer capacitors are largely determined by how fast the electrolyte ions can travel within the carbon electrode particles. Our systematic studies using zeolite-templated carbons show that an enhancement in ion transport rate by more than 2 orders of magnitude is possible by minimizing the micropore tortuosity. Very uniform carbon deposition was achieved using a well-controlled process involving the decomposition of acetylene precursor at a reduced pressure of 10 Torr and under a constant flow rate of 100 sccm. Selected carbon samples with well-aligned, straight micropores demonstrate high specific capacitance of up to 300 F/g and outstanding frequency response of up to 10 Hz for 250 microm thick electrodes, indicating an attractive combination of high specific energy and high specific power in electrical double layer capacitors. Such properties are critical for many peak-power hungry applications, such as the leveling of subsecond disturbances in power lines. Our findings provide guidance for the optimal design of porous carbons with greatly improved power storage characteristics.
Kinematics of the glenohumeral joint: Influences of muscle forces, ligamentous constraints, and articular geometry (1996)

Despite recent interest in the study of shoulder kinematics, there is considerable controversy in the literature regarding translations at the glenohumeral joint. The purpose of this study was to investigate the key factors that control shoulder motions, thus leading to a better understanding of joint function. Translation and rotation patterns were studied in fresh-frozen glenohumeral joints of human cadavers with a six-degrees-of-freedom magnetic tracking device. Shoulders were positioned from maximal internal to external rotation at several arm positions (various elevations and planes of motion). In order to determine the effect of muscle forces, joints were positioned both actively and passively. Additionally, articular surface geometry and ligament origin-insertion wrap lengths were measured to assess their influences on joint kinematics. When joints were positioned passively, large translations were observed at the extremes of motion. With active positioning, muscle forces tended to limit humeral head translations, principally by restricting rotational ranges of motion. However, when data from the passive model were reanalyzed by considering only the rotational ranges of motion seen actively, no significant differences in translation were found between the two models. Joint conformity was found to have a significant influence on translations during active positioning but not during passive positioning. Glenohumeral ligament wrap lengths, however, correlated with translations when joints were positioned passively but not when positioned actively. Findings from this study emphasize the importance of muscle forces in keeping the humeral head centered in the glenoid. Although large translations are possible, they can be achieved only with increases in rotational ranges of motion associated with the removal of muscle force. Additionally, joint conformity appears to play a role in controlling translations during active motions, whereas capsular constraints become more important during passive motions.
Techniques for Interactive Ray Tracing of Bézier Surfaces (2006)

We present a simple and generic algorithm for interactive ray tracing of free-form surfaces, allowing for a simple implementation for bicubic Bézier surfaces. The algorithm uses a fixed number of on-the-fly refinement steps to prevent crack appearance. Furthermore, we show that grouping rays into coherent bundles and tracing them together achieves a speed-up factor of more than 5 compared to tracing only single rays. Combining ray-bundle-based ray tracing with optimized kd-tree construction even allows for interactively ray tracing completely dynamic scenes with thousands of patches. Even highly complex scenes consisting of a million Bézier patches can be interactively ray traced while requiring only a few seconds startup time. Source code is available online.
Enantioselective Total Synthesis of (+)-Dibromophakellstatin (2003)

The first enantioselective total synthesis of (+)-phakellstatin and (+)-dibromophakellstatin was achieved. Key steps in the synthesis were a desymmetrization of the diketopiperazine (S,S)-cyclo (Pro, Pro) via a diastereoselective acylation, an intramolecular Mitsunobu reaction to introduce the C6 aminal, and a tandem Hofmann rearrangement/cyclization to simultaneously introduce the C10 quaternary aminal center and deliver the cyclic urea. The synthesis also demonstrates the unusual stability of pyrrolo aminals. Importantly, this strategy has the potential for producing phakellstatin derivatives, derived from (R,R)-cyclo (Pro, Pro), necessary for biological studies. A similar annulation protocol is also expected to be applicable to the synthesis of palau'amine.
Gate oxide damage reduction using a protective dielectric layer (1994)

Gate oxide damage from charge entering through the top surface of the gate electrode during plasma ashing, ion implantation, and LDD spacer oxide etching was measured using antenna structures. Significant charge damage to the 9.0 nm-thick gate oxide was detected for each of these processes. The damage was reduced by using a protective dielectric layer, in this case a thermally deposited TEOS oxide over the polycide gate electrode before gate definition. The dielectric appears to block charge penetration into the antenna. Damage can be reduced further by increasing the thickness of the dielectric layer; for a sufficiently thick layer (about 150 nm), charge entering through the top surface of the antenna was effectively eliminated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
IVF versus ICSI in sibling oocytes from patients with polycystic ovarian syndrome: a randomized controlled trial (2005)

Our results suggested that another randomized controlled study, randomizing patients instead of sibling oocytes, should be undertaken to compare the pregnancy rate per started cycle and to see whether ICSI should be performed on all, or at least on a portion of, oocytes for patients with PCOS undergoing IVF cycles.
Synthesis and Reactivity of Transition Metal Phosphoranides Having Three-Membered Phosphorus-Metal Nitrogen (or Oxygen) Rings (1987)

Abstract An account of our research on the synthesis and reactivity of transition metal phosphoranides having three-membered phosphorus-metal-nitrogen (or oxygen) ring is given. An attempt at acceeding to acyclic phosphoranide complexes from LiNR and CpFeL1L2X derivatives (L1 = CO, L2 = PR3; L1 = L2 =PR3; X2 = Cl, Br) resulted in the direct amination of the cyclopentadienyl ring. The influence of R, L and X on the issue of the reaction is discussed.