gebhart/patrepeval huggingface dataset:
Comparative Informatics Analysis to Evaluate Site-Specific Protein Oxidation in Multidimensional LC–MS/MS Data (2013)

Redox proteomics has yielded molecular insight into diseases of protein dysfunction attributable to oxidative stress, underscoring the need for robust detection of protein oxidation products. Additionally, oxidative protein surface mapping techniques utilize hydroxyl radicals to gain structural insight about solvent exposure. Interpretation of tandem mass spectral data is a critical challenge for such investigations, because reactive oxygen species target a wide breadth of amino acids. Additionally, oxidized peptides may be generated in a wide range of abundances since the reactivity of hydroxyl radicals with different amino acids spans 3 orders of magnitude. Taken together, these attributes of oxidative footprinting pose both experimental and computational challenges to detecting oxidized peptides that are naturally less abundant than their unoxidized counterparts. In this study, model proteins were oxidized electrochemically and analyzed at both the intact protein and peptide levels. A multidimensional chromatographic strategy was utilized to expand the dynamic range of oxidized peptide measurements. Peptide mass spectral data were searched by the "hybrid" software packages Inspect and Byonic, which incorporate de novo elements of spectral interpretation into a database search. This dynamic search capacity accommodates the challenge of searching for more than 40 oxidative mass shifts that can occur in a staggering variety of possible combinatorial occurrences. A prevailing set of oxidized residues was identified with this comparative approach, and evaluation of these sites was informed by solvent accessible surface area gleaned through molecular dynamics simulations. Along with increased levels of oxidation around highly reactive "hotspot" sites as expected, the enhanced sensitivity of these measurements uncovered a surprising level of oxidation on less reactive residues.
Human and mouse homo-oligomeric meprin A metalloendopeptidase: substrate and inhibitor specificities (2007)

Meprin metalloproteinases have been implicated in the susceptibility to and progression of diabetic nephropathy and inflammatory bowel diseases. Our studies with experimental models of these diseases in mice are congruent with the conclusion that meprins modulate the inflammatory responses and tissue damage. To determine whether the mouse and human enzymes differ, recombinant forms of meprin A from the two species were compared with respect to structure, substrates and inhibitors. Human homo-oligomeric meprin A formed oligomers ranging from 950,000 to 1,500,000 Da vs. 900,000 Da for mouse meprin A. Human and mouse meprin A exhibited similar activity against azocasein, fibronectin, collagen IV, and peptides such as parathyroid hormone, ghrelin, and gastrin-releasing peptide. The human enzyme had lower activity against gelatin, bradykinin, alpha-melanocyte-stimulating hormone and neurotensin, and higher activity against secretin and orcokinin. Human meprin A showed a preference for acidic residues in the P1' position of the substrate, unlike mouse meprin A. Several metalloproteinase inhibitors had IC(50) values in the nanomolar range, but potency ranged from similar values to a difference of several orders of magnitude for meprins from the two species. This work provides valuable data to improve predictability for human systems based on meprin functions in mouse models.
Startup strategies for mainstream anammox polishing in moving bed biofilm reactors (2022)

This study evaluated startup strategies for mainstream polishing anammox moving bed biofilm reactors (MBBRs) without anammox bacterial (AMX) biomass inoculation. Two types of startups were tested: anammox only (no external carbon addition) and partial denitrification/anammox (PdNA) with glycerol addition. Reactors were started with either virgin carriers or carriers with a preliminary biofilm from a mainstream aerobic integrated fixed-film activated sludge (IFAS) process. Three pilot-scale startups were completed under the following conditions: anammox-only with preliminary biofilm carriers, PdNA with preliminary biofilm carriers, and PdNA with virgin carriers. AMX presence was confirmed via quantitative polymerase chain reaction (qPCR) after 57, 57, and 77 days, respectively. Prior to AMX detection, average influent concentrations of ammonia and nitrite ranged from 1.7-2.7 mg/L and 0.98-1.8 mg/L, respectively. This study demonstrated that AMX can be grown on carriers without AMX seeding under mainstream conditions (temperature 17-29°C, low ammonia and nitrite), regardless of whether nitrite came from upstream or partial denitrification within the reactor. This study also showed that using preliminary biofilm carriers can decrease startup time by approximately 1 month. These results address critical questions for moving mainstream anammox processes to full-scale implementation, and suggest that PdNA MBBRs are feasible and sustainable for full-scale ammonia, nitrate, and nitrite polishing to meet stringent total nitrogen requirements. PRACTITIONER POINTS: This research will help utilities develop methods for starting up mainstream anammox MBBRs without the barrier of anammox biomass seeding. Preliminary biofilm carriers accelerated startup time in a PdNA MBBR, but a virgin carrier reactor started up in a similar timeframe, contrary to expectations. Also, contrary to expectations, high concentrations of ammonia and nitrite are not necessary for startup of an anammox or PdNA MBBR.
Low Temperature Growth of Bi<sub>4</sub>Ti<sub>3</sub>O<sub>12</sub> Thin Films by MOCVD and their Electrical Properties (1997)

We have developed a new low temperature growth technique of Bi4Ti3O12 thin films using MOCVD method, in which an ultra-thin double buffer layer (5nm-Bi4Ti3O12/5nm-TiO2) was used to control the crystallization and fine grain structure of Bi4Ti3O12 thin films. The 100nm-Bi4Ti3O12 thin films fabricated at 400°C showed an excellent smooth surface morphology and good electrical properties: large remanent polarization of Pr=11μC/cm2, coercive field of Ec=90kV/cm and low leakage current IL=7×10-9A/cm2 at 3V, respectively. In addition, for the first time the fatigue free property, which is very important for nonvolatile ferroelectric memories (NVFRAMs) applications, was confirmed up to 1×1012 switching cycles.
Long-term and large-scale multispecies dataset tracking population changes of common European breeding birds (2020)

Around fifteen thousand fieldworkers annually count breeding birds using standardized protocols in 28 European countries. The observations are collected by using country-specific and standardized protocols, validated, summarized and finally used for the production of continent-wide annual and long-term indices of population size changes of 170 species. Here, we present the database and provide a detailed summary of the methodology used for fieldwork and calculation of the relative population size change estimates. We also provide a brief overview of how the data are used in research, conservation and policy. We believe this unique database, based on decades of bird monitoring alongside the comprehensive summary of its methodology, will facilitate and encourage further use of the Pan-European Common Bird Monitoring Scheme results. The Pan-European Common Bird Monitoring Scheme database is organised into five datasets: (1) European species indices, (2) European species trends, (3) European species trends for three short periods, (4) a list of details on the national monitoring schemes and (5) a matrix of countries providing data for population size estimates of individual species. We aim to maintain the PECBMS database with annual updates. The annual updates will be available through the PECBMS database deposited at this Zenodo repository to ensure long-term public availability of the data.
Single-shot Layered Reflectance Separation Using a Polarized Light Field Camera (2016)

We present a novel computational photography technique for single shot separation of diffuse/specular reflectance as well as novel angular domain separation of layered reflectance. Our solution consists of a two-way polarized light field (TPLF) camera which simultaneously captures two orthogonal states of polarization. A single photograph of a subject acquired with the TPLF camera under polarized illumination then enables standard separation of diffuse (depolarizing) and polarization preserving specular reflectance using light field sampling. We further demonstrate that the acquired data also enables novel angular separation of layered reflectance including separation of specular reflectance and single scattering in the polarization preserving component, and separation of shallow scattering from deep scattering in the depolarizing component. We apply our approach for efficient acquisition of facial reflectance including diffuse and specular normal maps, and novel separation of photometric normals into layered reflectance normals for layered facial renderings. We demonstrate our proposed single shot layered reflectance separation to be comparable to an existing multi-shot technique that relies on structured lighting while achieving separation results under a variety of illumination conditions.
Can Machine Learning Help Identify Patients at Risk for Recurrent Sexually Transmitted Infections? (2020)

Machine algorithms using structured EHR data did not differentiate well between patients with and without repeat STIs diagnosis. Alternative strategies, able to account for sociobehavioral characteristics, could be explored.
High Power and High Reliable 915 nm Lasers with Window Structure Fabricated by Impurity Free Vacancy Disordering (IFVD) (2008)

We have demonstrated high performance broad area single emitter lasers with window structure fabricated by newly developed impurity free vacancy disordering (IFVD) technique. Vacancies induce quantum well intermixing, leading to bandgap shift. We have succeeded in obtaining the large bandgap shift in window region and maintaining the original bandgap in gain region simultaneously. We can control the bandgap difference. A very high output power of 25.6W at 30A under pulsed operation was obtained without facet degradation. This is the one of the highest power for 100μm wide single emitter lasers. Moreover, no degradation and no sudden failure were observed for 5800 hours life test at 8W-20°C. We have, thus, realized the highest output power and high reliable lasers with window structure fabricated by IFVD.
Implementation of the Car–Parrinello algorithm for ab initio total energy calculations on a massively parallel computer (1993)

An implementation of the Car–Parrinello algorithm for total energy pseudopotential calculations is undertaken on a massively parallel supercomputer, the Connection Machine CM-2. Its large memory and throughput makes feasible computations with systems involving more atoms than previously possible on conventional vector supercomputers. Calculations of the Takayanagi 7×7 reconstruction of the Si(111) surface demonstrate that computations involving 1000 atoms at realistic cutoff energies are now possible using ab initio techniques.
Development of fiber optic acoustic emission sensors (2001)

In this paper we describe the recently developed fiber optic (FO) acoustic emission (AE) sensors for NDE systems. FO sensors potentially offer much smaller size, reduced weight, the ability to operate at elevated temperatures, immunity to electromagnetic interference, resistance in corrosive environments, and the ability to multiplex multiple sensors on a single fiber. The response of the fiber optic AE sensors were also compared to conventional PZT AE sensors using standard pencil lead break tests. The results indicate that fiber optic AE sensors may provide sufficient sensitivity for some AE applications.
Two contact, 1 cm long, monolithic extended cavity laser actively mode-locked at 4.4 GHz (1992)

A 1.0 cm long, two contact, monolithic extended-cavity laser has been fabricated and actively mode-locked at a repetition rate of 4.4 GHz to produce 9.0 ps optical pulses. Doubling of the optical pulse repetition rate of 8.8 GHz without changing the sinusoidal drive frequency is achieved by synchronously modulating two separate active regions.
Evaluation of the Impact of Layout on Device and Analog Circuit Performance With Lateral Asymmetric Channel MOSFETs (2005)

Lateral asymmetric channel (LAC) or single halo devices have been reported to exhibit excellent short channel behavior in the sub-100-nm regime. In this paper, we have quantified the performance degradation in LAC devices due to fingered layouts. Our mixed-mode two-dimensional simulation results show that though the fingered layout of the device limits the performance of these MOSFETs, they still show superior performance over the conventional devices in the sub-100-nm channel length regime. We also present the simulation results of a two-stage operational amplifier with LAC and conventional devices using a 0.13-/spl mu/m technology with the help of look-up table simulations. Our results show that for the given design specifications, an OPAMP layout with conventional devices occupies 18% more chip area compared to the LAC device.
ChemInform Abstract: A FACILE ROUTE TO DIVINYLCYCLOPROPANES. AN EFFICIENT METHOD FOR THE ANNELATIVE FORMATION OF FUNCTIONALIZED CYCLOHEPTANES (1977)

Abstract Li‐vinylcyclopropane (II) reagieren mit dem 3‐Äthoxy‐2‐methyl‐2‐cyclopentenon (I) zu einem Addukt (III), das thermisch zum anellierten Cycloheptadien‐Derivat (IV) führt.
Hsp90 provides a platform for kinase dephosphorylation by PP5 (2023)

The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is activated by phosphorylation at specific regulatory sites. The cochaperone phosphatase PP5 dephosphorylates CRaf and Cdc37 in an Hsp90-dependent manner. Although dephosphorylating Cdc37 has been proposed as a mechanism for releasing Hsp90-bound kinases, here we show that Hsp90 bound kinases sterically inhibit Cdc37 dephosphorylation indicating kinase release must occur before Cdc37 dephosphorylation. Our cryo-EM structure of PP5 in complex with Hsp90:Cdc37:CRaf reveals how Hsp90 both activates PP5 and scaffolds its association with the bound CRaf to dephosphorylate phosphorylation sites neighboring the kinase domain. Thus, we directly show how Hsp90's role in maintaining protein homeostasis goes beyond folding and activation to include post translationally modifying its client kinases.
Challenges for on-chip optical interconnects (2005)

As integrated circuit interconnect dimensions continue to shrink and signaling frequencies increase, interconnect performance degrades. The performance degradation is due to several factors such as power consumption, cross-talk, and signal attenuation. On-chip optical interconnects are a potential solution to these scaling issues because they offer the promise of providing higher bandwidth. In this paper, progress on the major on-chip optical building blocks will be reviewed. It will be shown that significant advances have been made in the design and fabrication of waveguides, detectors, and couplers. However, major challenges in high speed electrical to optical conversion and signaling remain.
The pattern and distribution of immunoglobulin VH gene mutations in chronic lymphocytic leukemia B cells are consistent with the canonical somatic hypermutation process (2003)

The overexpanded clone in most B-cell-type chronic lymphocytic leukemia (BCLL) patients expresses an immunoglobulin (Ig) heavy chain variable (V(H)) region gene with some level of mutation. While it is presumed that these mutations were introduced in the progenitor cell of the leukemic clone by the canonical somatic hypermutation (SHM) process, direct evidence of such is lacking. Nucleotide sequences of the Ig V(H) genes from 172 B-CLL patients were analyzed. Previously described V(H) gene usage biases were noted. As with canonical SHM, mutations found in B-CLL were more frequent in RGYW hot spots (mutations in an RGYW motif = 44.1%; germ line frequency of RGYW motifs = 25.6%) and favored transitions over transversions (transition-transversion ratio = 1.29). Significantly, transition preference was also noted when only mutations in the wobble position of degenerate codons were considered. Wobble positions are inherently unselected since regardless of change an identical amino acid is encoded; therefore, they represent a window into the nucleotide bias of the mutational mechanism. B-CLL V(H) mutations concentrated in complementarity-determining region 1 (CDR1) and CDR2, which exhibited higher replacement-to-silent ratios (CDR R/S, 4.60; framework region [FR] R/S, 1.72). These results are consistent with the notion that V(H) mutations in B-CLL cells result from canonical SHM and select for altered, structurally sound antigen receptors.
Cheese Rheology and Texture (2002)

Cheese Rheology and Texture is the first reference to bring together the essential information on the rheological and textural properties of cheese and state-of-the-art measurement techniques.This comprehensive resource begins with an overview of cheesemaking technology and detailed descriptions of fundamental rheological test methods. Then
Representing and Reasoning About Space (2010)

This textbook for advanced undergraduates and graduate students emphasizes algorithms for a range of strategies for locomotion, sensing, and reasoning. It concentrates on wheeled and legged mobile robots but discusses a variety of other propulsion systems. This edition includes advances in robotics and intelligent machines over the ten years prior to publication, including significant coverage of SLAM (simultaneous localization and mapping) and multi-robot systems. It includes additional mathematical background and an extensive list of sample problems. Various mathematical techniques that were assumed in the first edition are now briefly introduced in appendices at the end of the text to make the book more self-contained. Researchers as well as students in the field of mobile robotics will appreciate this comprehensive treatment of state-of-the-art methods and key technologies.
Fluorescent Image Tracking Velocimetry of the Nimbus AxiPump (1993)

High shear rates and extended residence times causing hemolysis and platelet activation can develop in an assist pump or cannula when inferior flow conditions exist. The high volume output of a miniature axial flow pump presents challenges in avoiding these adverse conditions. To assess the hemodynamics within the continuous flow Nimbus Axi-Pump, vector flow fields inside a translucent inflow cannula and a modified 12 mm AxiPump were mapped. Fluorescent image tracking velocimetry was used to track the motion of neutrally buoyant fluorescent particles (30 microns) using pulsed laser light, high resolution video cameras, and computer image analysis. An acrylic pump housing and cannula were integrated into a mock circulatory loop filled with a Newtonian, optically clear blood analog fluid. The flow parameters were controlled to yield known, physiologic loading conditions, including varying degrees of pulsatility. Cannula flow visualization results exhibited critical recirculation patterns at the bend. These results will be used to further optimize the design of the inflow. Particle impact was seen at the pump inlet in the inducer region of the rotor. Very good attachment of flow from the rotor to stator was observed when the pump operated at normal operating speeds. Intermittent regurgitant flow fields were evident in the presence of increased pulsatility and low pump speed. These results have lead to improvements in impeller design and speed control criteria to avoid potential deleterious flows.
Chemotherapeutic Evaluation of a Synthetic Tubulysin Analogue–Dendrimer Conjugate in C26 Tumor Bearing Mice (2010)

Conjugate to ameliorate! Polymeric drug delivery using a synthetic tubulysin analogue in C26 tumor bearing mice is described. A single dose of this conjugate (shown) resulted in a 90 % increase in the average lifespan of the mice as compared to groups given a phosphate-buffered saline control or the free tubulysin analogue. Moreover, 37 % of the mice given the polymeric formulation were tumor free at the conclusion of the study.
The absorption of a mixture of amino acids by rat small intestine (1974)

1. The absorption of a mixture of amino acids by the small intestine has been studied in vitro with mucosal slices from rat jejunum. The mixture contained eighteen amino acids and was used at a concentration of 9.5 mM in the incubation medium. The uptake of fifteen of the amino acids was followed in each sample with the aid of an amino acid analyser.2. The endogenous amino acid content of the slices decreased during preparation and further substantial losses occurred when the slices were preincubated for 30 sec before the addition of the amino acid mixture to the incubation medium.3. When the slices were incubated with the amino acid mixture for 4.5 min all of the amino acid studied were accumulated to give concentration ratios of approximately 2.0.4. The amino acids were taken up rapidly by the tissue so that on average 82% of the amino acids absorbed in 4.5 min had already accumulated after one min of incubation.5. The data for individual amino acids revealed no obvious competition between the various amino acids, and the extent to which the various amino acids were accumulated by the tissue was proportional to their concentrations in the mixture.6. When the Na(+) in the incubation medium was replaced by Li(+), the slices accumulated all of the amino acids studied to concentrations significantly higher than those in the incubation medium. However, the concentration ratios obtained with the Li(+) medium were all lower than those obtained with the Na(+) medium and averaged slightly more than 1.5.7. When the Na(+) in the incubation medium was replaced by K(+) there was little amino acid accumulation, although concentration ratios significantly greater than one were achieved for aspartic acid, glycine, histidine and methionine.
Use of Free Space to Enhance the Performance, Energy Efficiency, and Fault-Tolerance of a File System (2009)

Abstract : This project has made several significant contributions in enhancing the energy efficiency, performance and fault-tolerance of computer storage systems. First, we developed Power-Aware Virtual Memory (PAVM) that finds and aggregates unmapped and unused memory pages. By powering down unused memory ranks, we can save a significant amount of energy dissipated by the main memory with virtually no performance degradation. Second, we developed the Free Space File System (FS2) based on the popular Ext2 file system by replicating temporally-related data blocks then using the free disk space to place these blocks closer to one another on the disk and thus allowing the disk heads to move less. This results in higher performance, lower energy consumption and higher fault-tolerance at almost zero cost. Finally, we characterized the disk failure patterns and used it to place replicas of critical information on the disk so as to protect them from common disk failures.
Genetic Determinants of Age-Related Macular Degeneration in Diverse Populations From the PAGE Study (2014)

While most associations did not generalize in the non-European populations, variants within lipid-related genes were found to be associated with AMD. This study highlights the need for larger well-powered studies in non-European populations.