gebhart/patrepeval huggingface dataset:
Uncoupling of Chromatin Assembly from DNA Replication in Sciara Reveals a Domain of Postreplicative Immature Chromatin (2021)

ABSTRACT DNA replication in dividing eukaryotic cells imposes a requirement for the faithful recreation on the newly synthesized chromatids of the nucleoprotein architecture of parent chromosomes. Practically nothing is known about the structure of postreplicative immature chromatin—a very short-lived entity (&lt; 30 min.). We report here the unexpected discovery that during DNA amplification of locus II/9A in salivary gland polytene chromosomes of the fungus fly Sciara coprophila , DNA replication fork passage is uncoupled from postreplicative chromatin assembly; this enables visualization and analysis of chromatin fibers disassembled by DNA replication. We used electron microscopy to visualize a wealth of low nucleosome density immature chromatin fibers in preparations of Sciara chromatin from amplification-stage tissue. Remarkably, as gauged by high sensitivity to micrococcal nuclease and an unusually short length of DNA associated with each histone octamer, we found that locus II/9A which undergoes amplification and is replicated once every 4-6 hrs.—but not the bulk genome or a replicatively quiescent DNA stretch—was maintained in such an ummature fiber for ca. 24 hrs. Following amplification, locus II/9A assumed conventional chromatin organization, indicating that the epigenetic mark targeting nascent DNA to the chromatin assembly machinery is stable for several hours. We propose that this very unusual prolonged maintenance of a segment of the genome in immature chromatin facilitates access by the basal transcriptional machinery to the amplified DNA, and thus is an evolutionary adaptation to the demand for high transcription from genes that reside in the amplified loci.
Abstract 13509: Cardiac Resynchronization Therapy in Patients With Atrial Fibrillation: The Certify Study (2013)

Objectives: To determine whether, in patients with atrial fibrillation (AF) undergoing cardiac resynchronization therapy (CRT), atrioventricular junction ablation (AVJA) is associated with a better outcome than treatment with rate-slowing drugs. Background: Different trial demonstrated that CRT is effective in heart failure (HF) patients who are in sinus rhythm (SR). No trials addressed whether CRT confers similar benefits in AF patients , with/without AVJA. Methods: The clinical outcome of CRT in patients with permanent AF undergoing CRT combined with either AVJA (n = 443) or rate-slowing drugs (n = 895) were compared with SR patients (n = 6,046). Results: Median follow-up of 37 months: total (6.8 vs 6.1 per 100 person year) and cardiac mortality (4.2 vs 4.0) (both p = NS) were similar in patients with AF+AVJA and patients in SR. In contrast, the AF+drugs group had a higher total and cardiac mortality than the SR and the AF+AVJA groups (11.3 and 8.1 , respectively; p Conclusions: Long term survival after CRT in patients with AF+AVJA is similar to that observed in patients in SR. Mortality is higher in AF patients treated with rate-slowing drugs.
Cleavage of lamin A by Mch2 alpha but not CPP32: multiple interleukin 1 beta-converting enzyme-related proteases with distinct substrate recognition properties are active in apoptosis. (1996)

Although proteases related to the interleukin 1 beta-converting enzyme (ICE) are known to be essential for apoptotic execution, the number of enzymes involved, their substrate specificities, and their specific roles in the characteristic biochemical and morphological changes of apoptosis are currently unknown. These questions were addressed using cloned recombinant ICE-related proteases (IRPs) and a cell-free model system for apoptosis (S/M extracts). First, we compared the substrate specificities of two recombinant human IRPs, CPP32 and Mch2 alpha. Both enzymes cleaved poly-(ADP-ribose) polymerase, albeit with different efficiencies. Mch2 alpha also cleaved recombinant and nuclear lamin A at a conserved VEID decreases NG sequence located in the middle of the coiled-coil rod domain, producing a fragment that was indistinguishable from the lamin A fragment observed in S/M extracts and in apoptotic cells. In contrast, CPP32 did not cleave lamin A. The cleavage of lamin A by Mch2 alpha and by S/M extracts was inhibited by millimolar concentrations of Zn2+, which had a minimal effect on cleavage of poly (ADP-ribose) polymerase by CPP32 and by S/M extracts. We also found that N-(acetyltyrosinylvalinyl-N epsilon-biotinyllysyl)aspartic acid [(2,6-dimethylbenzoyl)oxy]methyl ketone, which derivatizes the larger subunit of active ICE, can affinity label up to five active IRPs in S/M extracts. Together, these observations indicate that the processing of nuclear proteins in apoptosis involves multiple IRPs having distinct preferences for their apoptosis-associated substrates.
Optimizing Dynamic RAN Slicing in Programmable 5G Networks (2019)

Network slicing is envisioned as a tool for 5G networks to provide network flexibility and isolation among different logical networks. While network slicing is well investigated in the fixed-network side, in the Radio Access Network (RAN) there remain challenging problems, which originate mainly from the stochastic nature of the wireless channels and complex resource coupling between slices. In this work, we investigate a network slicing problem for the downlink RAN of a cellular network. Our target is the reduction of resource usage while guaranteeing slice isolation and simultaneously accounting for each slice's average rate and delay requirements. We tackle the problem with a Lyapunov optimization approach, leading to a simple resource assignment procedure that we can prove to achieve isolation while satisfying all slice guarantees. The proposed procedure leads to a functional split, where resources are scheduled within each slice by a slice manager, while a Software-Defined RAN (SD-RAN) controller dynamically re-assigns resources to each slice. We verify our approach through extensive simulations and provide insight on how to fine-tune available system parameters.
Amphiphilic Linear-branched Copolymers and Their Fluorinated Dendritic Analogs (1996)

Copolymers of PEG and analogs of second generation dendrimer have been synthesized and characterized. Normal polyether dendrimers can be replaced by other branched structures with similar physical properties. Incorporation of fluorinated chains enhance the hydrophobicity of the dendrimer. Attachment of long alkyl chains to dendrimers to achieve the same goal is under investigation and applications of the amphiphilic copolymers are being explored.
Supplementary Video S1 from Unexpected Activities in Regulating Ciliation Contribute to Off-target Effects of Targeted Drugs (2023)

&lt;p&gt;Supplementary Video S1. Time-lapse images of hTERT-RPE1-Arl13b-GFP cells starved in serum-free Opti-MEM for 48 hours.&lt;/p&gt;
A search for high-mass resonances decaying to τ+τ− in pp collisions at $$ \sqrt{s}=8 $$ TeV with the ATLAS detector (2015)

A bstract A search for high-mass resonances decaying into τ + τ − final states using proton-proton collisions at $$ \sqrt{s}=8 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>8</mml:mn> </mml:math> TeV produced by the Large Hadron Collider is presented. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 19.5–20.3 fb −1 . No statistically significant excess above the Standard Model expectation is observed; 95% credibility upper limits are set on the cross section times branching fraction of Z ′ resonances decaying into τ + τ − pairs as a function of the resonance mass. As a result, Z ′ bosons of the Sequential Standard Model with masses less than 2.02 TeV are excluded at 95% credibility. The impact of the fermionic couplings on the Z ′ acceptance is investigated and limits are also placed on a Z ′ model that exhibits enhanced couplings to third-generation fermions.
Insights into the surface composition and enrichment effects of ionic liquids and ionic liquid mixtures (2010)

A systematic study of ionic liquid surfaces by angle resolved X-ray photoelectron spectroscopy (ARXPS) is presented. By reviewing recent and presenting new results for imidazolium-based ionic liquids (ILs), we discuss the impact of chemical differences on surface composition and on surface enrichment effects. (1) For the hydrophilic ethylene glycol (EG) functionalised ILs [Me(EG)MIm][Tf(2)N], [Et(EG)(2)MIm][Tf(2)N] and [Me(EG)(3)MIm][Tf(2)N], which vary in the number of ethylene glycol units (from 1 to 3), we find that the surface composition of the near-surface region is in excellent agreement with the bulk composition, which is attributed to attractive interactions between the oxygen atoms on the cation to the hydrogen atoms on the imidazolium ring. (2) For [C(n)C(1)Im][Tf(2)N] (where n = 1-16), i.e. ILs with an alkyl chain of increasing length, an enrichment of the aliphatic carbons is observed for longer chains (n > 2), at the expense of the polar cation head groups and the anions in the first molecular layer, both of which are located approximately at the same distance from the outer surface. (3) To study the influence of the anion on the surface enrichment, we investigated ten ILs [C(8)C(1)Im][X] with the same cation, but very different anions [X](-). In all cases, surface enrichment of the cation alkyl chains is found, with the degree of enrichment decreasing with increasing size of the anion, i.e., it is most pronounced for the smallest anions and least pronounced for the largest anions. (4) For the IL mixture [C(2)C(1)Im][Tf(2)N] and [C(12)C(1)Im][Tf(2)N] we find a homogeneous distribution in the outermost surface region with no specific enrichment of the [C(12)C(1)Im](+) cation.
Bringing BLINK Closer to the Full Power of SQL. (2009)

ChiCTR-1800016531; Pre-results.
Regular TreeMap layouts for visual analysis of hierarchical data (2006)

Hierarchical relationships play an utmost important role in many application domains. The appropriate visualization of hierarchically structured data sets can contribute towards supporting the data analyst in effectively analyzing hierarchic structures using visualization as a user friendly means to communicate information. Information Visualization has contributed a number of useful techniques for visualization of hierarchically structured data sets. Yet, the support for certain regularity requirements as arising from many data element types has to be improved. In this paper, we analyze an existing variant of the popular TreeMap family of hierarchical layout algorithms, and we introduce a novel TreeMap algorithm supporting space efficient layout of hierarchical data sets providing global regular layouts. We detail our algorithm, and we present applications on a real-world data set as well as experiments performed on a synthetic data set, showing its applicability and usefulness.
Characterization and modeling of domain engineered relaxor ferroelectric single crystals (2004)

This work describes a measurement and modeling effort directed at improving our understanding of relaxor single crystals of PZN-xPT and PMN-xPT. Results include electromechanical characterization, crystal variant modeling, and modeling of field induced phase transitions. Key results include reducing high cycle fatigue by elimination of sharp comers on bulk specimens and development of engineered domain states other than [001] in rhombohedral compositions. The latter development coupled with the modeling work has led to identification and characterization of the [001] cut with properties optimized for d 31 and d 32 applications.
A novel tumor‐associated antigen, cell division cycle 45‐like can induce cytotoxic T‐lymphocytes reactive to tumor cells (2011)

The present study attempted to identify a useful tumor-associated antigen (TAA) for lung cancer immunotherapy and potential immunogenic peptides derived from the TAA. We focused on cell division cycle 45-like (CDC45L), which has a critical role in the initiation and elongation steps of DNA replication, as a novel candidate TAA for immunotherapy based on a genome-wide cDNA microarray analysis of lung cancer. The CDC45L was overexpressed in the majority of lung cancer tissues, but not in the adjacent non-cancerous tissues or in many normal adult tissues. We examined the in vitro and in vivo anti-tumor effects of cytotoxic T-lymphocytes (CTL) specific to CDC45L-derived peptides induced from HLA-A24 (A*24:02)-positive donors. We identified three CDC45L-derived peptides that could reproducibly induce CDC45L-specific and HLA-A24-restricted CTL from both healthy donors and lung cancer patients. The CTL could effectively lyse lung cancer cells that endogenously expressed both CDC45L and HLA-A24. In addition, we found that CDC45L (556) KFLDALISL(564) was eminent in that it induced not only HLA-A24 but also HLA-A2 (A*02:01)-restricted antigen specific CTL. Furthermore, the adoptive transfer of the CDC45L-specific CTL inhibited the growth of human cancer cells engrafted into immunocompromised mice. These results suggest that these three CDC45L-derived peptides are highly immunogenic epitopes and CDC45L is a novel TAA that might be a useful target for lung cancer immunotherapy.
Enabling Vaccine Delivery Platforms and Adjuvants for Malaria (2016)

Enabling vaccine delivery platforms and adjuvants with promising attributes for malaria vaccine development are reviewed within the framework of accessibility, efficacy, clinical status, cost, and cold-chain considerations. An emphasis is placed on commercially available platforms and adjuvants including virus-like particle, nanoparticle, microneedle, and mRNA vaccine delivery platforms as well as lipid vesicle, microparticle, and emulsion-based adjuvants. Strategies for addressing complications of vaccine delivery in endemic regions due to concatenate vaccination and infection, and parasite immune avoidance mechanisms are presented. Additionally, recent findings regarding how malaria infection triggers inflammatory pathways and T cell exhaustion along with negative impacts to the development of effective memory responses are described in a context relevant to vaccine development.
Frequent Silencing of Low Density Lipoprotein Receptor-Related Protein 1B (LRP1B ) Expression by Genetic and Epigenetic Mechanisms in Esophageal Squamous Cell Carcinoma (2004)

Low-density lipoprotein receptor-related protein 1B (LRP1B) is frequently deleted in tumors of various types, but its status and expression in esophageal squamous cell carcinomas (ESCs) have never been reported. In the course of a program to screen ESC cell lines for copy-number aberrations using array-based comparative genomic hybridization, we identified a homozygous deletion of LRP1B. Genomic PCR experiments revealed homozygous deletions of LRP1B in additional ESC cell lines (total, 6 of 43; 14.0%) and in primary esophageal tumors (30 of 70; 42.9%). Moreover, expression of LRP1B mRNA was frequently silenced in ESC lines without homozygous deletions (14 of 37; 37.8%). Using bisulfite-PCR analysis and sequencing, we found that LRP1B-nonexpressing cells without homozygous deletions were highly methylated at a CpG island of LRP1B, a sequence possessing promoter activity. Treatment with 5-aza-2'-deoxycytidine restored expression of LRP1B in those ESC lines. Histone acetylation status correlated directly with expression of LRP1B and inversely with the methylation status of the CpG island. Methylation of LRP1B was also detected in primary esophageal tumors. Restoration of LRP1B expression in ESC cells reduced colony formation. These results suggest that loss of LRP1B function in esophageal carcinogenesis most often occurs either by homozygous deletion or by transcriptional silencing through hypermethylation of its CpG island.
Structural Dependence of Physical Properties in Sodium Boroaluminosilicate Glasses (2012)

Boroaluminosilicate glasses have found applications in many fields. The extent and nature of the mixing of network formers like SiO2, B2O3, and Al2O3 play an important role in controlling the macroscopic properties. To understand the structure-property correlations in these glasses, we study a series of sodium boroaluminosilicate glasses with various [Al2O3]/[SiO2] ratios to access different regimes of sodium behavior. We determine dynamic properties, elastic moduli, and hardness of these glasses. The results reveal an existence of local minimum for density, fragility index, Young’s and shear moduli, and hardness around [Al2O3]-[Na2O]=0. Moreover, there exist three compositional response regions for elastic moduli and hardness. These results are explained in terms of topological constraint theory.
Supplementary Figure Legend from A Threshold Level of Intratumor CD8<sup>+</sup> T-cell PD1 Expression Dictates Therapeutic Response to Anti-PD1 (2023)

&lt;p&gt;Supplementary Figure Legend. Legends for Supplementary Figures S1-S8.&lt;/p&gt;
Power Optimization of Embedded Memory Systems via Data Remapping (2002)

In this paper, we provide a novel compile-time data remapping algorithm that runs in linear time. This remapping algorithm is the first fully automatic approach applicable to pointer-intensive dynamic applications. We show that data remapping can be used to significantly&#13;\nreduce the energy consumed as well as the memory size needed to meet a user-specified performance goal (i.e., execution time) -- relative to the same application executing without being remapped. These twin advantages afforded by a remapped program -- improved cache and energy&#13;\nneeds -- constitute a key step in a framework for design space exploration: for any given performance goal, remapping allows the user&#13;\nto reduce the primary and secondary cache size by 50%, yielding a concomitant energy savings of 57%. Additionally, viewed as a compiler optimization for a fixed processor, we show that remapping improves the energy consumed by the cache subsystem by 25%. All of the above&#13;\nsavings are in the context of the cache subsystem in isolation. We also show that remapping yields an average 20% energy saving for an ARM-like processor and cache subsystem. All of our improvements are achieved in the context of DIS, OLDEN and SPEC2000 pointer-centric benchmarks.
Functional Delineation of a Protein–Membrane Interaction Hotspot Site on the HIV-1 Neutralizing Antibody 10E8 (2022)

Antibody engagement with the membrane-proximal external region (MPER) of the envelope glycoprotein (Env) of HIV-1 constitutes a distinctive molecular recognition phenomenon, the full appreciation of which is crucial for understanding the mechanisms that underlie the broad neutralization of the virus. Recognition of the HIV-1 Env antigen seems to depend on two specific features developed by antibodies with MPER specificity: (i) a large cavity at the antigen-binding site that holds the epitope amphipathic helix; and (ii) a membrane-accommodating Fab surface that engages with viral phospholipids. Thus, besides the main Fab-peptide interaction, molecular recognition of MPER depends on semi-specific (electrostatic and hydrophobic) interactions with membranes and, reportedly, on specific binding to the phospholipid head groups. Here, based on available cryo-EM structures of Fab-Env complexes of the anti-MPER antibody 10E8, we sought to delineate the functional antibody-membrane interface using as the defining criterion the neutralization potency and binding affinity improvements induced by Arg substitutions. This rational, Arg-based mutagenesis strategy revealed the position-dependent contribution of electrostatic interactions upon inclusion of Arg-s at the CDR1, CDR2 or FR3 of the Fab light chain. Moreover, the contribution of the most effective Arg-s increased the potency enhancement induced by inclusion of a hydrophobic-at-interface Phe at position 100c of the heavy chain CDR3. In combination, the potency and affinity improvements by Arg residues delineated a protein-membrane interaction site, whose surface and position support a possible mechanism of action for 10E8-induced neutralization. Functional delineation of membrane-interacting patches could open new lines of research to optimize antibodies of therapeutic interest that target integral membrane epitopes.
Plug 'n Play Simplicity for Wireless Medical Body Sensors (2006)

Wireless medical body sensors are a key technology for unobtrusive health monitoring. The easy setup of such wireless body area networks is crucial to protect the user from the complexity of these systems. But automatically forming a wireless network comprising all sensors attached to the same body is challenging. We present a method for making wireless body-worn medical sensors aware of the persons they belong to by combining body-coupled with wireless communication. This enables a user to create a wireless body sensor network by just sticking the sensors to her body. A personal identifier allows sensors to annotate their readings with a user ID thereby ensuring safety in personal healthcare environments with multiple users
Latex Protein: A Hidden "Food" Allergen? (2000)

Avoidance of latex allergens is the primary method to prevent adverse reactions. Natural rubber latex is found in many different products in both the health care industry and in modern society, and consequently results in unexpected exposures of sensitized individuals. The use of latex gloves by food handlers provides one potential route for inadvertent exposure to latex allergens. In this study we have used two immunological methods to determine whether latex proteins are transferred to foods following contact with latex gloves. Direct transfer of latex protein to cheese was visualized using a modified immunoblot method. Sliced cheese was touched with a gloved finger. A nitrocellulose membrane was applied to lift the potential fingerprints and a rabbit anti-latex antiserum was used to visualize the transfer of any latex finger-prints. After handling lettuce with gloves, transferred protein was recovered by extracting the lettuce and quantified using an inhibition ELISA for latex proteins. Fingerprints of latex protein were readily detectable on cheese after contact with powdered latex gloves, but not with vinyl gloves. Furthermore, powdered latex glove use resulted in measurable amounts of latex protein on lettuce with an exposure-dependent increase in the latex protein levels. Lettuce alone or lettuce handled with vinyl gloves was negative for latex protein. The use of latex gloves by food handlers is the source of an indirect food additive in the form of latex proteins. It is recommended that food handlers avoid the use of latex gloves to eliminate inadvertent exposure of latex-sensitive individuals.
Deep Natural Language Processing for LinkedIn Search (2021)

Many search systems work with large amounts of natural language data, e.g., search queries, user profiles, and documents. Building a successful search system requires a thorough understanding of textual data semantics, where deep learning based natural language processing techniques (deep NLP) can be of great help. In this paper, we introduce a comprehensive study for applying deep NLP techniques to five representative tasks in search systems: query intent prediction (classification), query tagging (sequential tagging), document ranking (ranking), query auto completion (language modeling), and query suggestion (sequence to sequence). We also introduce BERT pre-training as a sixth task that can be applied to many of the other tasks. Through the model design and experiments of the six tasks, readers can find answers to four important questions: (1). When is deep NLP helpful/not helpful in search systems? (2). How to address latency challenges? (3). How to ensure model robustness? This work builds on existing efforts of LinkedIn search, and is tested at scale on LinkedIn's commercial search engines. We believe our experiences can provide useful insights for the industry and research communities.