gebhart/patrepeval huggingface dataset:
Field Division Routing (2010)

Multihop communication objectives and constraints impose a set of challenging requirements that create difficult conditions for simultaneous optimization of features such as scalability and performance. Routing in wireless multihop networks represents a crucial component of the overall network efficacy because it is a lower layer that enables the actual functionality of networks. We have developed field division routing (FDR), a distributed and nonhierarchical routing protocol that aims to coordinated addressing of scalability, topology alternations, latency, throughput, energy efficiency, and local storage requirements. FDR is based upon two optimization mechanisms: a reactive and focused diffusion that collects only network topology information directly required for making localized routing decisions, and a protocol for sharing routing information among neighboring nodes. Routing table initialization and maintenance are scalable in terms of both storage and overhead traffic necessary for building routing tables. FDR provides guaranteed connectivity while providing near-optimal all-node-pairs message delivery. The protocol is also power-efficient to a wide spectrum of topology changes that induce relatively few messages to update routing tables network-wide. We analyzed the new routing protocol both theoretically and using simulation.
Automated virtual network functions onboarding (2016)

Network functions virtualization (NFV) opens up a new ability of network enablement through agile network DevOps to design, develop, and test new services and to provide ongoing updates of existing services. This paper proposes a tool and methodology to aid the NFV designer to rapidly design and onboard new services and applications. Although the main focus is on the service design and onboarding, we provide the relation with other aspects such as management and orchestration, and service assurance of a complete lifecycle for network service. The proposed tool and methodology is called VNF Onboarding Automation Tool (VOAT). The prototype implementation is discussed as well as various use cases where VOAT has been used. With VOAT, an automated service design and onboarding can be efficiently achieved, hence reducing significantly the timeframe for deploying new services in telco cloud-based environment.
Substituted salicylic acid analogs offer improved potency against multidrug-resistant Neisseria gonorrhoeae and good selectivity against commensal vaginal bacteria (2023)

Abstract Drug-resistant Neisseria gonorrhoeae represents a major threat to public health; without new effective antibiotics, untreatable gonococcal infections loom as a real possibility. In a previous drug-repurposing study, we reported that salicylic acid had good potency against azithromycin-resistant N. gonorrhoeae . We now report that the anti-gonococcal activity in this scaffold is easily lost by inopportune substitution, but that select substituted naphthyl analogs ( 3b , o , p ) have superior activity to salicylic acid itself. Promisingly, these compounds also show very weak growth inhibition of commensal vaginal bacteria.
Tunable Microwave Photonic Notch Filter Using A 3?3 Coupler based Sagnac loop (2007)

We propose a simple and stable structure to realize a tunable negative coefficients microwave photonic notch filter. Theoretical analysis and experimental results are presented and show a good agreement.
Flexible backhaul-aware DBS-aided HetNet with IBFD communications (2019)

Drone-mounted base-stations (DBSs) are promising complements and substitutes of the terrestrial base-stations. We investigate the problem of Placement and cOmmunications in the DBS-aided heterogeneous network (POD) with tier-1 backhaul using free space optics communications and tier-2 backhaul utilizing in-band full-duplex communications to provide ubiquitous connections and high spectrum efficiency. The POD problem is shown to be NP-hard, and thus we simplify the POD problem by decomposing it into three sub-problems. Finally, we propose an approximation algorithm to solve the POD problem, and demonstrate that the proposed algorithm is superior to two baseline algorithms.
Supplementary Table 6B from AT13148 Is a Novel, Oral Multi-AGC Kinase Inhibitor with Potent Pharmacodynamic and Antitumor Activity (2023)

&lt;p&gt;XLS file - 62K, Gene Ontology (GO) analysis for genes significantly altered in expression by CCT128930 ranked according to the P-value of a modified Fisher's exact test (EASE score, DAVID) for enriched Gene Ontology terms&lt;/p&gt;
Abnormal Expression of the Plasma Cell Differentiation Factor X-Box Protein 1 (Xbp-1) in Waldenstrom’s Macroglobulinemia. (2005)

Abstract INTRODUCTION: Xbp-1 is a ubiquitously expressed basic leucine zipper protein which serves as key transcription factor for plasma cell differentiation and immunoglobulin production. XBP-1 mRNA undergoes splicing at an IRE-1a specific cleavage site to produce a spliced form (Xbp-1s) which due to a frame shift results in a more stable and potent transcription factor than the unspliced form (Xbp-1us). Previous observations demonstrated that Xbp-1 was highly expressed in multiple myeloma (MM), though its expression in other B-cell disorders including Waldenstrom’s macroglobulinemia (WM) remains to be clarified. METHODOLOGY: In this study, we investigated the different forms of Xbp-1 in CD19+ selected bone marrow (BM) cells from 61 patients with the consensus panel definition of WM using semi-quantitative PCR analysis. CD19+ selected BM cells from 6 healthy donors, and CD138+ selected BM cells from 4 MM patients were used as controls. All RT-PCR results were normalized to b-actin levels. Sequencing of Xbp-1 in CD19+ selected LPC was also performed for 20 WM patients. RESULTS: In 9/61 (15%) WM patients, Xbp-1 transcripts were undetectable. Among WM patients expressing Xbp-1, as well as all MM patients evaluated, higher levels of XBP-1us were observed in comparison to normal healthy donors (p=0.001). Decreased XBP-1s transcript levels were also observed among WM and MM patients versus healthy donors, but did not reach statistical significance. Sequence analysis of Xbp1 in CD19+ selected BM LPC demonstrated variants 10/20 WM patients in exon 1 that are currently under investigation. CONCLUSIONS: Abnormal expression of Xbp-1 is common in patients with WM, and includes loss of expression, and aberrations in splice patterns. The genetic basis for these findings is under investigation.
Baseline Features of the VICTORIA (Vericiguat Global Study in Subjects with Heart Failure with Reduced Ejection Fraction) Trial (2019)

VICTORIA comprises a broadly generalizable high-risk population of three unique clinical strata of worsening chronic HFrEF despite very good HF therapy. VICTORIA will establish the role of vericiguat, a soluble guanylate cyclase stimulator, in HFrEF.
Investigating the Heart Pump Implant Decision Process (2016)

Clinical decision support tools (DSTs) are computational systems that aid healthcare decision-making. While effective in labs, almost all these systems failed when they moved into clinical practice. Healthcare researchers speculated it is most likely due to a lack of user-centered HCI considerations in the design of these systems. This paper describes a field study investigating how clinicians make a heart pump implant decision with a focus on how to best integrate an intelligent DST into their work process. Our findings reveal a lack of perceived need for and trust of machine intelligence, as well as many barriers to computer use at the point of clinical decision-making. These findings suggest an alternative perspective to the traditional use models, in which clinicians engage with DSTs at the point of making a decision. We identify situations across patients' healthcare trajectories when decision supports would help, and we discuss new forms it might take in these situations.
Release, transformation, and risk factors of polybrominated diphenyl ethers from landfills to the surrounding environments: A review (2021)

Polybrominated diphenyl ethers (PBDEs) serve as brominated flame retardants when added to various products. When these products reach their end of life, a large amount of domestic waste containing PBDEs enters the landfills. Given their weak chemical bonds, they are easily affected by physical, chemical, and biological processes. These processes result in their release and the subsequent contamination of the surrounding soil, groundwater, and atmosphere, causing harm to humans and ecosystems. However, despite the progress made in the research of PBDEs over the years, understanding of the environmental behavior and fate of pollutants is still limited. With the development of cities, the release of PBDEs in old landfills will gradually increase the risk to the surrounding environment. Here we review the biological and nonbiological transformation of PBDEs and their derivatives in landfills and surrounding areas, as well as their distribution in soil, groundwater, and atmosphere. Specifically, this review aims to provide insights into the following aspects: 1) the biological (plant, animal, and microbial) and nonbiological (metal catalysis and photodegradation) conversion of PBDEs and their derivatives in landfills and surrounding areas; 2) the distribution of landfill-sourced PBDEs in the soil, groundwater, atmosphere and cross-media migration; and 3) suggestions and future research directions for the management and control of PBDEs in landfills.
Computation of protein–ligand binding free energies using quantum mechanical bespoke force fields (2019)

A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein. Promising agreement between theory and experiment highlights the potential for future use of system-specific force fields in computer-aided drug design.
ChemInform Abstract: Ammonium Metavanadate: A Novel Catalyst for Synthesis of 2‐Substituted Benzimidazole Derivatives. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Artificial intelligence framework identifies candidate targets for drug repurposing in Alzheimer’s disease (2022)

In summary, we present an integrated, network-based artificial intelligence methodology to rapidly translate GWAS findings and multi-omics data to genotype-informed therapeutic discovery in AD.
RAPTOR: A Five-Safes approach to a secure, cloud native and serverless genomics data repository (2022)

Abstract Genomic researchers are increasingly utilizing commercial cloud platforms (CCPs) to manage their data and analytics needs. Commercial clouds allow researchers to grow their storage and analytics capacity on demand, keeping pace with expanding project data footprints and enabling researchers to avoid large capital expenditures while paying only for IT capacity consumed by their project. Cloud computing also allows researchers to overcome common network and storage bottlenecks encountered when combining or re-analysing large datasets. However, cloud computing presents a new set of challenges. Without adequate security controls, the risk of unauthorised access may be higher for data stored on the cloud. In addition, regulators are increasingly mandating data access patterns and specific security protocols on the storage and use of genomic data to safeguard rights of the study participants. While CCPs provide tools for security and regulatory compliance, utilising these tools to build the necessary controls required for cloud solutions is not trivial as such skill sets are not commonly found in a genomics lab. The Research Assets Provisioning and Tracking Online Repository (RAPTOR) by the Genome Institute of Singapore is a cloud native genomics data repository and analytics platform focusing on security and regulatory compliance. Using a “five-safes” framework (Safe Purpose, Safe People, Safe Settings, Safe Data and Safe Output), RAPTOR provides security and governance controls to data contributors and users leveraging cloud computing for sharing and analysis of large genomic datasets without the risk of security breaches or running afoul of regulations. RAPTOR can also enable data federation with other genomic data repositories using GA4GH community-defined standards, allowing researchers to boost the statistical power of their work and overcome geographic and ancestry limitations of data sets
Supplementary Methods and Figures 1 - 6 from Systemic Delivery of <i>Salmonella typhimurium</i> Transformed with IDO shRNA Enhances Intratumoral Vector Colonization and Suppresses Tumor Growth (2023)

&lt;p&gt;PDF file - 221K, Supplemental Figs: 1. Transformation of VNP20009 with shIDO does not enhance its infectivity 2. ShIDO-ST reduces the formation of melanoma lung metastases. 3. Frequency of Gr1+CD11b+ cells in organs of tumor-bearig mice receiving PBS, shScr-ST, or shIDO-ST treatment. 4. Apoptotic CD45+ subsets in tumors of shIDO-ST treated mice includes CD4+ and CD8+ cells. 5. Hypoxia alone does not induce apoptosis in shIDO-ST-infected B16F10 cells. 6. ShIDO-ST treatment suppresses subcutaneous (s.c.) Pan02 tumor growth in C57BL/6 mice. Supplemental Methods: Flow cytometry and statistics&lt;/p&gt;
Additive electroplating technology as a post-CMOS process for the production of MEMS acceleration-threshold switches for transportation applications (2000)

This paper presents an acceleration-threshold sensor fabricated with an electroplating technology which can be integrated on top of a pre-processed CMOS signal processing circuit. The device can be manufactured using a standard low-cost CMOS production line and then adding the mechanical sensor elements via a specialized back-end process. This makes the system especially interesting for automotive applications, such as airbag safety systems or transportation shock monitoring systems, where smaller size, improved functionality, high reliability and low costs are important.
Transseptal direct complete annuloplasty: early experience (2021)

Annuloplasty is a fundamental component of surgical mitral valve repair, and is employed in nearly 100% of repair operations for both primary and secondary mitral regurgitation (SMR). Developing transcatheter techniques to replicate surgical annuloplasty has been the focus of significant innovation and development in recent years. Since many patients are not offered surgery due to high perceived surgical risk, transcatheter approaches will provide new treatment options. In this manuscript, we review technologies which allow transseptal and transcatheter mitral valve (MV) annuloplasty.
Genetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production (2017)

Abstract The pentose phosphate pathway (PPP) plays an important role in the efficiency of xylose fermentation during cellulosic ethanol production. In simultaneous saccharification and co-fermentation (SSCF), the optimal temperature for cellulase hydrolysis of lignocellulose is much higher than that of fermentation. Successful use of SSCF requires optimization of the expression of PPP genes at elevated temperatures. This study examined the combinatorial expression of PPP genes at high temperature. The results revealed that over-expression of TAL1 and TKL1 in Saccharomyces cerevisiae (S. cerevisiae) at 30 °C and over-expression of all PPP genes at 36 °C resulted in the highest ethanol productivities. Furthermore, combinatorial over-expression of PPP genes derived from S. cerevisiae and a thermostable yeast Kluyveromyces marxianus allowed the strain to ferment xylose with ethanol productivity of 0.51 g/L/h, even at 38 °C. These results clearly demonstrate that xylose metabolism can be improved by the utilization of appropriate combinations of thermostable PPP genes in high-temperature production of ethanol.
Chronic Pancreatitis in the 21st Century - Research Challenges and Opportunities (2016)

A workshop was sponsored by the National Institute of Diabetes and Digestive and Kidney Diseases to focus on research gaps and opportunities in chronic pancreatitis (CP) and its sequelae. This conference marked the 20th year anniversary of the discovery of the cationic trypsinogen (PRSS1) gene mutation for hereditary pancreatitis. The event was held on July 27, 2016, and structured into 4 sessions: (1) pathophysiology, (2) exocrine complications, (3) endocrine complications, and (4) pain. The current state of knowledge was reviewed; many knowledge gaps and research needs were identified that require further investigation. Common themes included the need to design better tools to diagnose CP and its sequelae early and reliably, identify predisposing risk factors for disease progression, develop standardized protocols to distinguish type 3c diabetes mellitus from other types of diabetes, and design effective therapeutic strategies through novel cell culture technologies, animal models mimicking human disease, and pain management tools. Gene therapy and cystic fibrosis conductance regulator potentiators as possible treatments of CP were discussed. Importantly, the need for CP end points and intermediate targets for future drug trials was emphasized.
Immunogenicity of Mycoplasma pneumoniae Glycolipids: A Novel Approach to the Production of Antisera to Membrane Lipids (1970)

The glycolipid haptens of Mycoplasma pneumoniae were bound to membrane proteins of acholeplasma laidlawii (formerly Mycoplasma laidlawii) by reaggregation. This process consisted of the solubilization of lipid-depleted A. laidlawii membranes and M. pneumoniae glycolipids in 20 mM sodium dodecyl sulfate, and dialysis of the mixed solutions against 20 mM Mg(2+). The hybrid reaggregate, collected by centrifugation, was highly immunogenic in rabbits, eliciting the production of a high titer of antibodies that fixed complement with the purified glycolipids and inhibited the metabolism of M. pneumoniae cells. The free glycolipids, or their mixture with A. laidlawii proteins, were much less effective in stimulating these antibodies. The antibodies to the hybrid reaggregate agglutinated M. pneumoniae cells and inhibited their ability to absorb erythrocytes, which indicates that at least some of the serologically-active glycolipids are exposed at the outer membrane surface. The ability to bind selected membrane lipids to membrane proteins of a serologically unrelated species provides a new tool for producing antibodies to lipid haptens.
Decreased susceptibility of melanized Cryptococcus neoformans to UV light (1994)

Melanized Cryptococcus neoformans cells were less susceptible than nonmelanized cells to the fungicidal effects of UV light. Phenoloxidase-catalyzed production of melanin-like pigments may serve to protect the fungus against ionizing radiation.
RETRACTED: The Cf-9 Disease Resistance Protein Is Present in an ∼420-Kilodalton Heteromultimeric Membrane-Associated Complex at One Molecule per Complex. (2017)

The tomato Cf-9 gene confers race-specific resistance to the fungal pathogen Cladosporium fulvum expressing the corresponding avirulence gene Avr9. In tobacco, Cf-9 confers a hypersensitive response to the Avr9 peptide. To investigate Cf-9 protein function in initiating defense signaling, we engineered a functional C-terminal fusion of the Cf-9 gene with the TAP (Tandem Affinity Purification) tag. In addition, we established a transient expression assay in Nicotiana benthamiana leaves for the production of functional Cf-9:myc and Cf-9:TAP. Transiently expressed Cf-9:myc and Cf-9:TAP proteins induced an Avr9-dependent hypersensitive response, consistent with previous results with stably transformed tobacco plants and derived cell suspension cultures expressing c-myc-tagged Cf-9. Gel filtration of microsomal fractions solubilized with octylglucoside revealed that the Cf-9 protein, either as c-myc or TAP fusions, migrated at a molecular mass of 350 to 475 kD. By using blue native gel electrophoresis, the molecular size was confirmed to be approximately 420 kD. Our results suggest that only one Cf-9 protein molecule is present in the Cf-9 complex and that Cf-9 is part of a membrane complex consisting of an additional glycoprotein partner(s). The high structural similarity between Cf proteins and Clavata2 (CLV2) of Arabidopsis, together with the similarity of molecular mass between Cf-9 and CLV complexes (420 and 450 kD, respectively), led us to investigate whether Cf-9 is integrated into membrane-associated protein complexes like those formed by CLV1 and CLV2. Unlike CLV2, the Cf-9 protein did not form disulfide-linked heterodimers, no ligand (Avr9)-dependent shift in the molecular mass of the Cf-9 complex was detected, and no Rho-GTPase-related proteins were found associated with Cf-9 under the conditions tested. Thus, Cf-9-dependent defense signaling and CLV2-dependent regulation of meristem development seem to be accomplished via distinct mechanisms, despite the structural similarity of their key components Cf-9 and CLV2.
Using process dissection to achieve design for manufacturability for electronic assemblies (2003)

A DFM (design for manufacturability) concept called PPM dissection that uses the assembly defect rates in p.p.m.'s from measurements of variables controllable in the design phase is described. The material presented is on a most basic level, i.e. without the extensive equations and algorithms that make it work. A simple example is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cross correlation of chemical shift anisotropy and dipolar interactions in methyl protons investigated by selective nuclear magnetic resonance spectroscopy (1993)

A group spin approach is used to describe the interconversion of magnetization modes in systems of three equivalent spins 1/2. It is shown that the most prominent effect of cross correlation of the fluctuations of chemical shift anisotropy and dipolar interactions is the transformation of two-quantum coherences of second rank into third rank coherences. A novel experiment is described which allows one to observe such a process.
Action exemplar based real-time action detection (2009)

We propose a real-time action detection system based on a novel action representation and an effective learning method with a small training set. We represent actions with a new feature that measures the ¿global¿ distance from a set of action exemplars, where action exemplars are constructed from a vocabulary that encodes ¿local¿ instantaneous body motions. A cascade of linear SVM is used to learn target actions, where at each layer a selective set of exemplars is chosen and variations between locally similar actions are trained in a coarse to fine manner. The method is further extended to incrementally learn a new action with a single example. The method is implemented as a real-time system that can detect actions at frame rate. The performance is extensively validated by evaluating on public and in-house action datasets.