gebhart/patrepeval huggingface dataset:
PGFinder, a novel analysis pipeline for the consistent, reproducible, and high-resolution structural analysis of bacterial peptidoglycans (2021)

Many software solutions are available for proteomics and glycomics studies, but none are ideal for the structural analysis of peptidoglycan (PG), the essential and major component of bacterial cell envelopes. It icomprises glycan chains and peptide stems, both containing unusual amino acids and sugars. This has forced the field to rely on manual analysis approaches, which are time-consuming, labour-intensive, and prone to error. The lack of automated tools has hampered the ability to perform high-throughput analyses and prevented the adoption of a standard methodology. Here, we describe a novel tool called PGFinder for the analysis of PG structure and demonstrate that it represents a powerful tool to quantify PG fragments and discover novel structural features. Our analysis workflow, which relies on open-access tools, is a breakthrough towards a consistent and reproducible analysis of bacterial PGs. It represents a significant advance towards peptidoglycomics as a full-fledged discipline.
Learning Anaphoricity and Antecedent Ranking Features for Coreference Resolution (2015)

Sam Wiseman, Alexander M. Rush, Stuart Shieber, Jason Weston. Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2015.
CMOS Integrated Nanophotonics for future computing systems (2011)

CMOS Integrated Nanophotonics allows ultra-dense monolithic single-chip integration of optical and electrical functions. This technology can enable future Exaflops supercomputers by connecting racks, modules, and chips together with ultra-low power massively parallel optical interconnects.
Polyarteritis nodosa of the epididymis in a patient with Whipple's disease. (1987)

The case of a 55-year-old white male who developed necrotizing arteritis localized to the superior pole of the epididymis is presented. He had a history of Whipple's disease and euthyroid Graves' disease. Histopathologic section of an extratesticular mass showed a necrotizing vasculitis with giant cells; periodic acid Schiff stain for Whipple "bacilli" was negative. The combination of rare diseases in our patient suggests the possibility of a common infectious or immune etiology, perhaps mediated via circulating immune complexes.
A systematic approach for system bus load reduction applied to medical imaging (2002)

Multimedia algorithms deal with enormous amounts of data transfers and storage, resulting in huge bandwidth requirements at the off-chip memory and system bus level. As a result the related energy consumption becomes critical. Even for execution time the bottleneck can shift from the CPU to the external bus load. This paper demonstrates a systematic software approach to reduce this system bus load. It consists of source-to-source code transformations, that have to be applied before the conventional ILP compilation. To illustrate this we use a cavity detection algorithm for medical imaging, that is mapped on a general-purpose programmable processor.
Nested Transactions, Conflict-Based Locking, and Dynamic Atomicity. (1987)

Abstract : In this paper examines some concurrency control algorithms for nested transaction systems. A simple local property called dynamic atomicity is defined for data objects in such a system, and we show that all the executions of a system are serially correct (despite concurrency and transaction aborts) provided each data object is dynamic atomic. This result is applied to give a correctness proof for a new algorithm, called Conflict Based Locking, for managing data in a nested transaction system. The algorithm uses a table specifying which operations may not proceed concurrently to determine when an operation may be granted a lock on an object. The algorithm is an extension of a general conflict-based locking protocol introduced by Weihl for transaction systems without nesting. It is also similar to Moss' algorithm, which uses read- and write- locks and a stack of versions of each object to ensure the serializability and recoverability of transactions accessing the data. We show that objects implemented using Moss' algorithm of the new Conflict-Based Locking algorithm are dynamic atomic. Thus it follows that if each object in a nested transaction system uses either Moss' algorithm or the new Conflict-Based Locking algorithm, then all executions of the system will be serially correct.
Supplementary Table 2B from Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes (2023)

&lt;p&gt;Dual Sequence capture of high risk HPV in TrDNA aligned to all high risk HPV types and low risk HPV types from PaVE database.&lt;/p&gt;
The Effect of Cation Mixing in LiNiO2 toward the Oxygen Evolution Reaction (2020)

Abstract Nickel‐based oxide catalysts are widely used for the oxygen evolution reaction (OER) in alkaline water electrolysis because of their low cost and high activity. In particular, the LiNiO 2 catalyst shows high activity. Therefore, to elucidate the fundamental relationship between the local structure, catalyst activity, and stability of LiNiO 2 , we investigated the cation mixing effect by mixing sites of lithium and nickel ions in the LiNiO 2 ‐based catalysts. Lower degrees of cation mixing lead to higher intrinsic OER activity but lower long‐term stability. The X‐ray absorption spectra (XAS) displayed a strong hybridization state of the Ni 3d and O 2p orbitals, which is the origin of the different catalytic activity behaviors. Meanwhile, operando XAS studies combined with potentiostatic stability tests and inductively coupled plasma optical emission spectrometry (ICP‐OES) demonstrated the Li ion loss during the OER process. Thus, the instability of LiNiO 2 originates from de‐intercalation of Li ions and this irreversible structure change deteriorates the performance. Hindering the lithium diffusion path by cation mixing is a useful strategy for maintaining performance. This strategy could provide a novel design principle for compatible high activity and long‐lasting catalysts by reasonable structure mediation.
2.2 Cotton fibers as natural raw materials for cellulose acetate production (2004)

Abstract The commercially available cotton species are only three botanical species. For these species, the cotton fibers were described to consist of two different types of fibers termed “lint” and “linter”. The structure and chemical constituents of these cotton fibers were compared, so as to use them judiciously as natural raw materials for cellulose acetate production.
Puromycin‐based purification of rat brain capillary endothelial cell cultures. Effect on the expression of blood–brain barrier‐specific properties (2005)

One of the main difficulties with primary rat brain endothelial cell (RBEC) cultures is obtaining pure cultures. The variation in purity limits the achievement of in vitro models of the rat blood-brain barrier. As P-glycoprotein expression is known to be much higher in RBECs than in any contaminating cells, we have tested the effect of five P-glycoprotein substrates (vincristine, vinblastine, colchicine, puromycin and doxorubicin) on RBEC cultures, assuming that RBECs would resist the treatment with these toxic compounds whereas contaminating cells would not. Treatment with either 4 microg/mL puromycin for the first 2 days of culture or 3 microg/mL puromycin for the first 3 days showed the best results without causing toxicity to the cells. Transendothelial electrical resistance was significantly increased in cell monolayers treated with puromycin compared with untreated cell monolayers. When cocultured with astrocytes in the presence of cAMP, the puromycin-treated RBEC monolayer showed a highly reduced permeability to sodium fluorescein (down to 0.75 x 10(-6) cm/s) and a high electrical resistance (up to 500 Omega x cm(2)). In conclusion, this method of RBEC purification will allow the production of in vitro models of the rat blood-brain barrier for cellular and molecular biology studies as well as pharmacological investigations.
T2-weighted BOLD fMRI at 9.4 T using a S2-SSFP-EPI sequence (2013)

It has been hypothesized that T2-weighted BOLD fMRI at ultra-high field shows higher spatial specificity than T2*-weighted BOLD, since the main signal contribution is expected to come from the extravascular spins of the microvasculature. Unfortunately, the number of slices that can be acquired in multi-slice SE-EPI is limited at ultra-high field due to SAR constraints. T2-weighted steady-state sequences, such as S2-SSFP, have been previously used as an alternative to spin-echo based BOLD fMRI. In this work, we present a 3D S2-SSFP sequence that is accelerated using an EPI readout and show first results from finger tapping experiments at 9.4 T.
Highly Stable Double-Gate Ga–In–Zn–O Thin-Film Transistor (2010)

We report the electrical stability of double-gate (DG) Ga-In-Zn-O thin-film transistors (TFTs). The threshold voltage ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">VT</i> ) shift of the DG TFT after 3 h of positive-bias temperature stress ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GS</sub> = + 20 V, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> = + 0.1 V, and Temperature = 60°C) is as small as +2.7 V, while that of a conventional single-gate (SG) TFT is +6.6 V. The results of negative-bias temperature stress [(NBTS); <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">GS</sub> = - 20 V, <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> = + 10 V, and Temperature = 60°C] are more dramatic: The <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">VT</i> shift of the DG TFT is only +0.1 V, whereas that of the SG TFT is -9.1 V. With backlight illumination, the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">VT</i> shift of the SG TFT under the same NBTS becomes severe ( -11.1 V). However, it remains as small as -0.7 V for the DG TFT.
Fixed-order H<sup>&#x221E;</sup> controller design via HIFOO, a specialized nonsmooth optimization package (2008)

We report on our experience with fixed-order Hfr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">infin</sup> controller design using the HIFOO toolbox. We applied HIFOO to various benchmark fixed (or reduced) order Hfr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">infin</sup> controller design problems in the literature, comparing the results with those published for other methods. The results show that HIFOO can be used as an effective alternative to existing methods for fixed-order Hfr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">infin</sup> controller design.
Wiskott-Aldrich Syndrome Protein Induces Actin Clustering without Direct Binding to Cdc42 (1999)

WASP (Wiskott-Aldrich syndrome protein) was identified as the gene product whose mutation causes the human hereditary disease Wiskott-Aldrich syndrome. WASP contains many functional domains and has been shown to induce the formation of clusters of actin filaments in a manner dependent on Cdc42. However, there has been no report investigating what domain(s) is(are) important for the function. Here we present for the first time the results of detailed analyses on the domain-function relationship of WASP. First, the C-terminal verprolin-cofilin-acidic domain was shown to be essential for the regulation of actin cytoskeleton. In addition, we found that the clustering of WASP itself is distinct from actin clustering. The partial protein containing the region from the N-terminal pleckstrin homology domain to the basic residue-rich region also clustered especially around the nucleus as wild type WASP without inducing actin clustering. Finally, we obtained the quite unexpected result that a WASP mutant deficient in binding to Cdc42 still induced actin cluster formation, indicating that direct interaction between Cdc42 and WASP is not required for the regulation of actin cytoskeleton. This result may explain why no Wiskott-Aldrich syndrome patients have been identified with a missense mutation in the Cdc42-binding site.
Molecular Understanding of Development of Ductal Pancreatic Cancer (2018)

Ductal adenocarcinoma of the pancreas, also known as “pancreatic cancer,” is among the deadliest of all of the solid malignancies. Significant efforts have therefore been exerted to advance our understanding of the fundamental biology of ductal adenocarcinomas, and to apply this knowledge to improving patient care and to ultimately reducing patient mortality. At the DNA level, ductal adenocarcinomas are characterized by activating somatic mutations in an oncogene, KRAS, and by inactivating somatic mutations in three tumor suppressor genes: TP53, SMAD4, and p16/CDKN2A. A number of other genes are mutated in a minority of ductal adenocarcinomas, and some of these low prevalence genes have clinical significance and are therefore important to understand. Ductal adenocarcinomas are also distinguished by significant changes in gene and protein expression, and some of these changes are actively being exploited clinically. It is our hope that a better molecular understanding of the development of ductal adenocarcinoma will soon lead to significant improvements in patient survival.
Probing active‐site residues of pyranose 2‐oxidase from Trametes multicolor by semi‐rational protein design (2009)

D-Tagatose is a sweetener with low caloric and non-glycemic characteristics. It can be produced by an enzymatic oxidation of D-galactose specifically at C2 followed by chemical hydrogenation. Pyranose 2-oxidase (P2Ox) from Trametes multicolor catalyzes the oxidation of many aldopyranoses to their corresponding 2-keto derivatives. Since D-galactose is not the preferred substrate of P2Ox, semi-rational design was employed to improve the catalytic efficiency with this poor substrate. Saturation mutagenesis was applied on all positions in the active site of the enzyme, resulting in a library of mutants, which were screened for improved activity in a 96-well microtiter plate format. Mutants with higher activity than wild-type P2Ox were chosen for further kinetic investigations. Variant V546C was found to show a 2.5-fold increase of k(cat) with both D-glucose and D-galactose when oxygen was used as electron acceptor. Because of weak substrate binding, however, k(cat)/K(M) is lower for both sugar substrates compared to wild-type TmP2Ox. Furthermore, variants at position T169, i.e., T169S and T169N, showed an improvement of the catalytic characteristics of P2Ox with D-galactose. Batch conversion experiments of D-galactose to 2-keto-D-galactose were performed with wild-type TmP2O as well as with variants T169S, T169N, V546C and V546C/T169N to corroborate the kinetic properties determined by Michaelis-Menten kinetics.
ChemInform Abstract: Stereoselective Synthesis of β‐2‐Deoxyribonucleosides from 1‐O‐Acetyl‐3‐O‐(2‐(methylsulfinyl)ethyl)‐2‐deoxyribose. (1989)

Abstract The title reaction is performed by coupling the deoxyribose derivatives (I) with the activated alkaloids (II), (IV), or (VIII) in the presence of trimethylsilyl triflate.
View interpolation based multiple description coding of multiview images (2009)

Albeit multiple description coding is a hot topic in compressed image/video transmission, there has not been extensive research on MDC for multiview data. In this paper, a multiview image multiple description coding scheme is proposed by combining rectification based view interpolation and encoding prediction residue. The joint optimal bit allocation of several components in our system is also discussed and its performance is analyzed. Compared with the method on view subsampling, the simulation results show that the proposed scheme can offer significant improvement, especially at high bit rate. And, the experimental results reveal that the proposed method can outperform the JMVC prediction based method over more than 1 dB in term of side distortion, given the same bit rate and central distortion.
Distributed cooperation in the absence of communication (brief announcement) (2000)

This work studies a distributed cooperation problem under an extreme assumption that no two processors may be able to communicate during a prolonged period of time. For problems where the quality of distributed decision-making depends on, and can be traded for, communication, the solution space needs to consider the possibility of no communication. Notably, this is the case in the load-balancing setting introduced by Papadimitriou and Yanakakis [PY] and studied by Georgiades, Mavronicolas and Spirakis [GMS]. The distributed cooperation problem that we consider here is defined for n processors in terms of t tasks that need to be performed efficiently and that are known to all processors. The fact that the tasks are initially known makes it possible for the problem to be solved in the absence of communication. The efficiency requirement and the possibility of eventual availability of communication make it desirable to structure the work of the processors so that when eventually some processors are able to communicate, the amount of wasted (redundant) work they have collectively performed prior to that time is controlled. We model solutions to the problem as sets of n lists of distinct tasks from {1,… ,t}. We call such lists schedules. We define and study the notion of k-waste that, for a set of n schedules, measures the maximum number of redundant task identifiers contained in any subset of k (≤ n) schedules. We are interested in expressing k-waste as a function of the length of schedules. Our goal is to construct n schedules of length t such that k-waste is controlled for any prefixes of the schedules.
Design and implementation of user interactive wireless smart home energy management system (2013)

Electricity usage is increasing day by day due to the changing life style of home user and an increase in appliances in the home area network. Our proposed home energy management system for home users will monitor, manage and control the usage of home appliances, by reducing the monthly electricity bill. The proposed wireless architecture consists of an appliance control device called Wireless Enabled Electricity Manager (WEEMAN) installed next to a switch board or every device/appliance in a room. The central node called smart meter runs an algorithm called Availability Based Energy Management algorithm. This algorithm learns about the previous usage patterns of the appliances, collects real time power consumption of appliances from WEEMAN to generate efficient energy load patterns. The highpoint of the algorithm is that it gives an option for the user to set their monthly current bill and pro-actively control the operation of all the appliances according to the amount. We have developed a hardware test bed consisting of WEEMAN connected to some selected appliances and a smart meter to control every WEEMAN.
Mechanism of bisphosphonate-related osteonecrosis of the jaw (BRONJ) revealed by targeted removal of legacy bisphosphonate from jawbone using competing inert hydroxymethylene diphosphonate (2022)

Bisphosphonate-related osteonecrosis of the jaw (BRONJ) presents as a morbid jawbone lesion in patients exposed to a nitrogen-containing bisphosphonate (N-BP). Although it is rare, BRONJ has caused apprehension among patients and healthcare providers and decreased acceptance of this antiresorptive drug class to treat osteoporosis and metastatic osteolysis. We report here a novel method to elucidate the pathological mechanism of BRONJ by the selective removal of legacy N-BP from the jawbone using an intra-oral application of hydroxymethylene diphosphonate (HMDP) formulated in liposome-based deformable nanoscale vesicles (DNV). After maxillary tooth extraction, zoledronate-treated mice developed delayed gingival wound closure, delayed tooth extraction socket healing and increased jawbone osteonecrosis consistent with human BRONJ lesions. Single cell RNA sequencing of mouse gingival cells revealed oral barrier immune dysregulation and unresolved proinflammatory reaction. HMDP-DNV topical applications to nascent mouse BRONJ lesions resulted in accelerated gingival wound closure and bone socket healing as well as attenuation of osteonecrosis development. The gingival single cell RNA sequencing demonstrated resolution of chronic inflammation by increased anti-inflammatory signature gene expression of lymphocytes and myeloid-derived suppressor cells. This study suggests that BRONJ pathology is related to N-BP levels in jawbones and demonstrates the potential of HMDP-DNV as an effective BRONJ therapy.
Use of prostate cancer subtyping by gene expression to predict response to radiation and chemohormonal therapies. (2023)

241 Background: We previously reported on the use of gene expression profiling to characterize four primary subtypes in an analysis of over 100,000 prostate cancer primary tumors. Here we examine these subtypes and response to radiation (RT) after prostatectomy or chemotherapy in addition to androgen deprivation therapy (ADT) in hormone-sensitive metastatic prostate cancer (mHSPC). Methods: We examined a 215-gene prostate subtyping classifier (PSC) which groups luminal and basal gene expression profiles into one of four subtypes; luminal differentiated (LD), luminal proliferating (LP), basal immune (BI) and basal neuroendocrine-like (BN). The log-rank method was used to compare (i) metastasis-free survival between patients who did and did not receive salvage RT in the META855 cohort of localized disease patients treated with radical prostatectomy (n=855) and the (ii) overall survival of patients on the Phase III mHSPC EA3805 CHAARTED trial of ADT or ADT + docetaxel chemotherapy (n=160). Results: After radical prostatectomy, patients with BI tumors derived benefit from RT in terms of metastasis-free survival ( P=9.23e-4) while those with other subtype tumors did not (Each Log-rank P≥0.5). Patients with metastatic disease and LP tumors derived benefit from docetaxel (Log-rank P=0.002) while those with other subtypes tumors did not (Log-rank P=0.2). Conclusions: Basal-luminal subtyping segments tumors by relevant biological processes with potential implications for identifying patients who benefit from salvage radiation post prostatectomy and addition of docetaxel to ADT in mHSPC.