gebhart/patrepeval huggingface dataset:
MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion (2020)

Mass spectrometry-based proteomics technologies are prime methods for the high-throughput identification of proteins in complex biological samples. Nevertheless, there are still technical limitations that hinder the ability of mass spectrometry to identify low abundance proteins in complex samples. Characterizing such proteins is essential to provide a comprehensive understanding of the biological processes taking place in cells and tissues. Still today, most mass spectrometry-based proteomics approaches use a data-dependent acquisition strategy, which favors the collection of mass spectra from proteins of higher abundance. Since the computational identification of proteins from proteomics data is typically performed after mass spectrometry analysis, large numbers of mass spectra are typically redundantly acquired from the same abundant proteins, and little to no mass spectra are acquired for proteins of lower abundance. We therefore propose a novel supervised learning algorithm, MealTime-MS, that identifies proteins in real-time as mass spectrometry data are acquired and prevents further data collection from confidently identified proteins to ultimately free mass spectrometry resources to improve the identification sensitivity of low abundance proteins. We use real-time simulations of a previously performed mass spectrometry analysis of a HEK293 cell lysate to show that our approach can identify 92.1% of the proteins detected in the experiment using 66.2% of the MS2 spectra. We also demonstrate that our approach outperforms a previously proposed method, is sufficiently fast for real-time mass spectrometry analysis, and is flexible. Finally, MealTime-MS' efficient usage of mass spectrometry resources will provide a more comprehensive characterization of proteomes in complex samples.
A 1.5-dB Insertion Loss, 34-dBm P<sub>1dB</sub> Power Modulator with 46% Fractional Bandwidth in 45-nm CMOS SOI (2019)

This work reports a high-power modulator implemented in 45-nm CMOS SOI for signal processing after the power amplifier. Two stacked switch variations, a 12 stack and 8 stack, were designed in 45-nm SOI CMOS and tested for trade-offs in insertion loss and power handling. These switches use a novel tapering technique to significantly improve switch linearity. The modulators have P <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> values between 34 dBm and 39 dBm while demonstrating a modulation bandwidth of nearly 500 MHz with a 1 GHz carrier. The IIP3 is between 46 dBm and 61 dBm.
Risk factors of unexplained early neurological deterioration after treatment for ischemic stroke due to large vessel occlusion: a post hoc analysis of the HERMES study (2022)

UnEND is not an uncommon event, with a similar rate which ever treatment arm is considered. In the clinical scenario of AIS due to large vessel occlusion, no patient-related factor seems to increase the risk for UnEND when treated by EVT compared with MM.
Realization and optimization of a 1 ns pulsewidth multi-stage 250 kW peak power monolithic Yb doped fiber amplifier at 1064 nm (2017)

We present a simple way to achieve and optimize hundreds of kW peak power pulsed output using a monolithic amplifier chain based on solid core double cladding fiber tightly packaged. A fiber pigtailed current driven diode is used to produce nanosecond pulses at 1064 nm. We present how to optimize the use of Fabry-Perot versus DFB type diode along with the proper wavelength locking using a fiber Bragg grating. The optimization of the two pre-amplifiers with respect to the pump wavelength and Yb inversions is presented. We explain how to manage ASE using core and cladding pumping and by using single pass and double pass amplifier. ASE rejection within the Yb fiber itself and with the use of bandpass filter is discussed. Maximizing the amplifier conversion efficiency with regards to the fiber parameters, glass matrix and signal wavelength is described in details. We present how to achieve high peak power at the power amplifier stage using large core/cladding diameter ratio highly doped Yb fibers pumped at 975 nm. The effect of pump bleaching on the effective Yb fiber length is analyzed carefully. We demonstrate that counter-pumping brings little advantage in very short length amplifier. Dealing with the self-pulsation limit of stimulated Brillouin scattering is presented with the adjustment of the seed pulsewidth and linewidth. Future prospects for doubling the output peak power are discussed.
Panax Ginseng C.A.Mey. as Medicine: The Potential Use of Panax Ginseng C.A.Mey. as a Remedy for Kidney Protection from a Pharmacological Perspective (2021)

Panax ginseng C.A.Mey. has been widely consumed as food/diet supplements from natural sources, and its therapeutic properties have also aroused widespread concern. Therapeutic properties of Panax ginseng C.A.Mey. such as anti-inflammatory, ameliorating chronic inflammation, enhancing the immunity, resisting the oxidation again, and regulating the glucose and lipid metabolism have been widely reported. Recent years, lots of interesting studies have reported the potential use of Panax ginseng C.A.Mey. in the management of DKD. DKD has become the leading cause of end-stage renal disease worldwide, which increases the risk of premature death and poses a serious financial burden. Although DKD is somehow controllable with different drugs such as Angiotensin-Converting Enzyme Inhibitors (ACEI), Angiotensin Receptor Blockers (ARB) and lowering-glucose agents, modern dietary changes associated with DKD have facilitated research to assess the preventive and therapeutic merits of diet supplements from natural sources as medicine including Panax ginseng C.A.Mey. Findings from many scientific evidences have suggested that Panax ginseng C.A.Mey. can relieve the pathological status in cellular and animal models of DKD. Moreover, a few studies showed that alleviation of clinical phenotype such as reducing albuminuria, serum creatinine and renal anemia in DKD patients after application or consumption of Panax ginseng C.A.Mey.. Therefore, this review aims to discuss the effectiveness of Panax ginseng C.A.Mey. as medicine for targeting pathological phenotypes in DKD from a pharmacological perspective. This review will provide new insights into the potential understanding use of Panax ginseng C.A.Mey. in the management of DKD in clinical settings.
Observations on the relationship between nerve supply and hair positioning in the rat vibrissa follicle. (1984)

The present study has demonstrated an anatomical relationship between the position of the growing and non-growing hairs of the rat vibrissa follicle and the point where the follicular nerve supply penetrates the follicle capsule circumference. This finding may be significant in relation to the sensory function of the follicle, as physiological data have shown that the degree of stimulation of brain cells following mechanical displacement of the whisker is direction dependent. The observed relationship between the nerve entry point and the hairs, therefore, may reflect an uneven distribution of nerve endings around the upper follicle circumference. In relation to hair growth, the above observation requires that the non-growing club hair must consistently move up one side of the follicle at the end of each growth cycle. A possible clue as to the mechanism by which club hair movement is directed can be derived from observation of asymmetry, both at the base of the club hair, and in the epidermal matrix near the end of the growth cycle.
Inhibition of two gluconeogenic enzymes by glycosyl-phosphatidylinositol: a model for insulin action (1994)

Conference Article| February 01 1994 Inhibition of two gluconeogenic enzymes by glycosyl-phosphatidylinositol: a model for insulin action SAM P HEYWOOD; SAM P HEYWOOD 1Department of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K. Search for other works by this author on: This Site PubMed Google Scholar NIGEL M. HOOPER NIGEL M. HOOPER 1Department of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1994) 22 (1): 10S. https://doi.org/10.1042/bst022010s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation SAM P HEYWOOD, NIGEL M. HOOPER; Inhibition of two gluconeogenic enzymes by glycosyl-phosphatidylinositol: a model for insulin action. Biochem Soc Trans 1 February 1994; 22 (1): 10S. doi: https://doi.org/10.1042/bst022010s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: CRD, cross-reacting determinant, F-1,6-BPase, fructose-1,6-bisphosphatase, GPI, glycosyl-phosphatidylinositol This content is only available as a PDF. © 1994 Biochemical Society1994 Article PDF first page preview Close Modal You do not currently have access to this content.
Supplementary Figures 1 - 7 from Gut Microbiota Protects against Gastrointestinal Tumorigenesis Caused by Epithelial Injury (2023)

&lt;p&gt;PDF file - 615K, Increased mortality of GF mice with high concentrations of DSS (S1); Tumors in GF mice have similar nuclear beta-catenin localization as tumors in SPF mice (S2); Percent weight change from baseline (start of DSS) for GF and SPF mice with AOM and 1.5% DSS (S3); Increased inflammatory cell recruitment in SPF mice early after DSS-induced intestinal injury (S4); Tumors in GF mice have similar proliferative activity as tumors in SPF mice (S5); Recolonization of GF mice with the gut microbiota reduces mortality to DSS (S6); Recolonization of GF mice with the gut microbiota restores ability of GF mice to induce reparative inflammation (S7).&lt;/p&gt;
A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA (2007)

This paper studies several designs of network-based FPGA implementation of a stochastic simulation algorithm called the next reaction method, known for its large number of calculation involved. The procedure is divided into several subdivisions which will be implemented as independent modules, and they are connected with configurable interconnection networks so as to provide high throughput. By performing a multi-threading simulation, 3.6 times speedup was obtained compared with an execution on general purpose processors.
Two-year follow-up from the phase 3 KEYNOTE-045 trial of pembrolizumab (pembro) vs investigator’s choice (paclitaxel, docetaxel, or vinflunine) in recurrent, advanced urothelial cancer (UC). (2018)

410 Background: Based on interim results from the phase 3 KEYNOTE-045 (NCT02256436) study comparing pembro v investigator’s choice of chemotherapy (chemo), pembro was approved for the treatment of locally advanced or metastatic UC that has progressed during or after a platinum-containing regimen. Updated results after 2 years of follow-up are presented. Methods: Eligible patients (histologically or cytologically confirmed UC, progression after platinum, ECOG PS 0-2, measurable disease per RECIST v1.1, ≤2 lines of systemic therapy) were randomly assigned 1:1 to pembro 200 mg Q3W or investigator’s choice of paclitaxel 175 mg/m 2 Q3W, docetaxel 75 mg/m 2 Q3W, or vinflunine 320 mg/m 2 Q3W. Primary efficacy end points were OS and PFS (RECIST v1.1, blinded central review). ORR (RECIST v1.1, blinded central review) was a secondary end point. Results: As of Oct 26, 2017, among the 542 enrolled patients (pembro, 270; chemo, 272), median follow-up was 27.7 mo. Median OS was significantly longer with pembro v chemo (10.3 v 7.3 mo; HR, 0.70; P &lt; 0.0002). OS benefit with pembro v chemo was seen in all PD-L1 expression subgroups (HR: combined positive score [CPS] &lt; 1, 0.82; CPS ≥1, 0.58; CPS &lt; 10, 0.75; CPS ≥10, 0.56) and was maintained regardless of age, ECOG PS, prior therapy, liver metastases, baseline hemoglobin, time from last chemo, histology, risk factor group, and choice of chemo. PFS was not different between arms (2.1 v 3.3 mo; HR, 0.96; P = 0.32). ORR was higher with pembro v chemo (21.1% v 11.0%). Median duration of response was longer with pembro (not reached [1.6+–30.3+ mo] v 4.4 mo [1.4+–29.9+ mo]), and a greater proportion of responses lasted ≥12 mo (68% v 35%) as assessed by Kaplan-Meier method. Fewer patients with pembro v chemo experienced a treatment-related adverse event of any grade (62.0% v 90.6%) and a grade ≥3 adverse event (16.5% v 50.2%). Conclusions: Results observed over 2 years of follow-up, including OS benefit and superior safety with pembro v chemo, were consistent with the interim analyses that led to the approval of pembro in locally advanced or metastatic UC that progressed during or after platinum-based chemotherapy. Clinical trial information: NCT02256436.
Simple motor and phonemic processing reaction times of elderly subjects. (1986)

Simple motor reaction time (RT) was measured for arm movement in response to a known monosyllable presented by earphone. The required direction of movement (L or R) was known to S. Choice RT was also measured: only one word of a pair of taped monosyllabic words, differing only in the prevocalic consonant (e.g., tea-key) was presented by earphone. Simultaneously, a picture of each word appeared on response plates, one to the L and one to the R of the center rest position. S had to touch the response plate with the picture of the word heard. Subtracting simple from choice RT, in msec, yielded an estimate of auditory-phonemic processing (decoding) time. Data were collected from generally normal, healthy, elderly Ss [Grp I (10 M, 10 F) of 72 yrs mean age, and Grp II (7 M, 9 F) of 84 yrs mean age] and a control group (9 M, 9 F) of 21 yrs mean age. An ANOVA with repeated measures showed that significant differences existed among the 3 groups. A similar ANOVA procedure on phonemic processing time revealed that significant differences existed between the younger and the older Ss, but not between Grps I vs II. Collectively, these findings were taken to suggest that advanced age does not affect all behavioral operations in a generalized fashion. It was suggested that auditory-phonemic processing is more resistant to the aging process than manual responses.
Genetic Evidence Supports Species Delimitation of <i>Luidia</i> in the Northern Gulf of Mexico (2022)

AbstractAccurate species delimitation is crucial to understanding biodiversity. In the northern Gulf of Mexico, recent genetic evidence has suggested that the tricolor <i>Luidia lawrencei</i> is not a species distinct from the gray <i>Luidia clathrata</i>. We collected <i>Luidia</i> specimens from Apalachee Bay, Florida, and morphologically identified 11 as <i>L. clathrata</i> and 16 as <i>L. lawrencei</i>. We sequenced 1074 bp of the cytochrome <i>c</i> oxidase subunit I (<i>COI</i>) and found ~14% divergence between <i>L. clathrata</i> and <i>L. lawrencei</i>, suggesting two distinct species (within-species divergence was <1%). Two specimens were phenotypically <i>L. lawrencei</i> (<i>i.e.</i>, tricolor morph) but mitochondrially were <i>L. clathrata</i>. Our findings lend support to maintaining <i>L. clathrata</i> and <i>L. lawrencei</i> as distinct species. However, the species boundary between these two taxa may be porous, and ongoing hybridization may occur when the two species are found in sympatry. Future work with nuclear markers is warranted to determine the frequency of hybridization and the extent of introgression. Clarifying the genetic relationship between these species will provide a baseline for assessing ongoing changes in connectivity of these two highly abundant sea stars in the rapidly warming northern Gulf of Mexico.
Methanol Synthesis from Industrial CO2 Sources: A Contribution to Chemical Energy Conversion (2017)

CO2 hydrogenation as a route for the chemical energy storage over a commercial Cu/ZnO/Al2O3 catalyst has been studied. To check the optimal conditions for an efficient methanol production the influence of temperature and space velocity on the catalytic performance has been demonstrated. Time-on-stream measurements in the absence and the presence of benzene in the gas feed mixture were performed to investigate the possibility to use alternative carbon sources, which contain traces of aromatics. The catalyst can operate in a stable way without the presence of carbon monoxide in the feed, which means that increased water contents in the product gas cannot destroy the catalyst’s performance completely. The presence of benzene in the feed does not lead to a deactivation of the catalyst. With these findings methanol production starting from exhaust gases from steel mills seems to become an interesting alternative for sustainable methanol production.
Polypeptide Composition of Paired Helical Filaments (1989)

Immunocytochemical studies using antibodies to cytoskeletal proteins have provided conflicting data on the components of paired helical filaments (PHF), due solely to immunological cross-reactivities. To avoid such ambiguity, we developed a protein chemical approach to the identification of the PHF components. After treatment with formic acid, PHF were digested with lysylendopeptidase and the resultant peptides were separated by HPLC. All major peaks were analysed for their amino acid compositions and sequences. From the PHF digest, proteolytic fragments of ubiquitin, tau and beta protein were sequenced. Ubiquitin in PHF appears to be in a conjugated form, while its target protein remains unidentified. Tau is integrated into PHF at the site of its carboxyl third. The presence of beta protein fragments is best interpreted as being due to contamination of amyloid filaments in the PHF preparation. Thus, ubiquitin and tau are the two definite components of PHF.
Expediting Assessment of Damaged Buildings during Disaster Response Using Mobile Ad Hoc Networks (2009)

The complexity of planning after a catastrophic incident is significantly influenced by disruption of critical infrastructure like transportation and telecommunication systems, making it very difficult to achieve a credible common operating picture to respond to the disaster. To increase situational awareness, it is important for first responders to acquire and share building information like structural damage and probability of further collapse of buildings at the disaster site. Current paper-based communications take 24 to 48 hours (or longer) to reach command centers causing response activities to begin without an assessment of critical needs. This paper proposes a framework that allows structural engineers to seamlessly exchange critical information about affected buildings with first responders based on establishment of Mobile Ad Hoc Network (MANET). In a mobile wireless ad hoc network, computers (nodes) in the network cooperate to forward packets for each other, due to the limited wireless transmission range of each individual node. Since MANET do not require any communication infrastructure, they are ideal for communicating during disasters. Adopting such a framework will help planners prioritize search and rescue operations more effectively.
Radiation-induced transforming growth factor beta and subsequent extracellular matrix reorganization in murine mammary gland. (1993)

Little is known about radiation-induced protein expression in vivo nor has the relationship between early molecular events and subsequent tissue repair, fibrosis, or carcinogenesis been fully appraised. In this study, expression of proteins involved in tissue remodeling was examined in mammary gland immediately and shortly after ionizing radiation exposure. Using indirect immunofluorescence, selected antigens were followed as a function of time after 0, 5, or 10 Gy of whole body gamma-radiation in the mammary gland of adult female BALB/c mice. Rapid induction of transforming growth factor beta (TGF beta) immunoreactivity was observed at 1 h post radiation. Extracellular and intracellular TGF beta increased in the periepithelial stromal sheath as evidenced by immunoreactivity with antibodies CC(1-30) and LC(1-30), respectively. Furthermore, both extracellular and intracellular TGF beta were unexpectedly expressed in the previously negative adipose stroma. Elevated expression persisted for 7 days after irradiation. Thus an early response to radiation exposure is the induction of TGF beta, which mediates myriad events during tissue repair, growth, and extracellular matrix production. The distribution of extracellular matrix proteins was examined as a function of time post radiation exposure. Collagen III immunoreactivity decreased in the periepithelial stroma at day 1. In contrast, at day 3 collagen III was newly evident in the adipose stroma, and periepithelial collagen III had increased in both abundance and intensity. By day 7 collagen III expression in the adipose stroma had resolved but was enhanced in the periepithelial stroma. Over this same period stromal collagen I immunoreactivity surrounding the epithelium became diffuse and possibly diminished. Fibronectin, laminin, and collagen IV localization were unchanged over the time course. I postulate that radiation-induced TGF beta may mediate the remodeling of the stromal extracellular matrix in the irradiated mammary gland.
An Enantioselective Approach to the Taxanes: Direct access to functionalized <i>cis</i>‐tricyclo[9.3.1.0<sup>3,8</sup>]pentadecanes <i>via</i> α‐hydroxy ketone and <i>Wagner</i>‐<i>Meerwein</i> rearrangements (1992)

Abstract The feasibility of the titled reactions for the rapid, enantioselective synthesis of cis ‐tricyclo[9.3.1.0 3,8 ]pentadecane precursors to taxusin and taxol has been examined. The catalysts most well suited to inducing the appropriate 1,2‐shifts have been identified. To a great extent, the rearrangement products are formed as a direct consequence of appropriate structural features (kinetic phenomenon) and strain minimization (thermodynamic driving force). Complementary MM2 calculations of the global minimum in each series provided indications that were completely in line with the experimental observations. Sophisticated NMR studies and X‐ray crystallographic determinations were coordinated to remove any ambiguity of product structure and solid‐state conformation.
A Queuing Model for a Hybrid Data Multiplexer (1979)

There are several instances in a data network where a communication line is shared by two or more types of data. In this paper, we analyze the performance of a buffer used to multiplex two types of data. Sporadic short messages, like inquiries from terminals, share the same channel as relatively steady synchronous data, like trunk traffic or long messages from computer data bases. To the authors' knowledge, previous studies have been limited to an ad hoc approximation to the probability distribution of interest. We solve for the equilibrium distribution of number of units of data in the buffer. The delay distribution easily follows. Numerical results are also presented which can be used as a guide to determining how much of each type of traffic can be sustained simultaneously.
Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression (2020)

SMM is a genetically mature entity whereby most driver genetic alterations have already occurred, which suggests the existence of a right-skewed model of genetic evolution from monoclonal gammopathy of undetermined significance to MM. We identified and externally validated genomic predictors of progression that could distinguish patients at high risk of progression to MM and, thus, improve on the precision of current clinical models.