gebhart/patrepeval huggingface dataset:
Semiflexible Immunobrushes Induce Enhanced T Cell Activation and Expansion (2021)

A variety of bioactive materials developed to expand T cells for adoptive transfer into cancer patients are currently evaluated in the clinic. In most cases, T cell activating biomolecules are attached to rigid surfaces or matrices and form a static interface between materials and the signaling receptors on the T cells. We hypothesized that a T cell activating polymer brush interface might better mimic the cell surface of a natural antigen-presenting cell, facilitating receptor movement and concomitant advantageous mechanical forces to provide enhanced T cell activating capacities. Here, as a proof of concept, we synthesized semiflexible polyisocyanopeptide (PIC) polymer-based immunobrushes equipped with T cell activating agonistic anti-CD3 (αCD3) and αCD28 antibodies placed on magnetic microbeads. We demonstrated enhanced efficiency of <i>ex vivo</i> expansion of activated primary human T cells even at very low numbers of stimulating antibodies compared to rigid beads. Importantly, the immunobrush architecture appeared crucial for this improved T cell activating capacity. Immunobrushes outperform current benchmarks by producing higher numbers of T cells exhibiting a combination of beneficial phenotypic characteristics, such as reduced exhaustion marker expression, high cytokine production, and robust expression of cytotoxic hallmarks. This study indicates that semiflexible immunobrushes have great potential in making T cell-based immunotherapies more effective.
Sol-gel approaches for solid electrolytes and electrode materials (1995)

Abstract Sol-gel chemistry has a great many potential applications in the preparation of unique electrochemical materials, from non-equilibrium transition metal oxides which may be of use as high energy density electrodes, to high surface area mixed oxides which may possess high proton conductivity, to novel composite structures consisting of inorganic gels in combination with organic electronic and ionic conductors. This papar reviews prior work on proton conduction in gel systems and presents recent work regarding electrode materials prepared by sol-gel methods and inorganic-organic materials.
When is azoospermia not azoospermia? (2008)

Men with azoospermia, defined as no sperm in the ejaculate as documented by semen analysis, either have an obstruction to the excretory ductal system or defective spermatogenesis. The observation that more than 60% of men with defective spermatogenesis may have pockets of spermatogenesis within the testis1,2 provides hope that many of these “azoospermic” patients can potentially be fathers with testicular sperm extraction (TESE) or testicular sperm aspiration (TESA) together with intracytoplasmic sperm injection and in vitro fertilization, provided these “pockets” of sperm, which theoretically never make it out of the ductal system, can be successfully harvested. TESE in these nonobstructive azoospermic patients requires either the use of a microscope to find the sperm (micro-TESE) or multiple incision sites in 1 or both testes in the search for these pockets of sperm.3 TESA also requires multiple aspirations in these azoospermic patients, although the success rate with TESA may not be as high as with TESE.4,5 In addition, there is never any guarantee that any of these pockets of sperm will be found when either of these 2 procedures is performed.
What's the Difference? The potential for Convolutional Neural Networks for transient detection without template subtraction (2022)

We present a study of the potential for Convolutional Neural Networks (CNNs) to enable separation of astrophysical transients from image artifacts, a task known as "real-bogus" classification without requiring a template subtracted (or difference) image which requires a computationally expensive process to generate, involving image matching on small spatial scales in large volumes of data. Using data from the Dark Energy Survey, we explore the use of CNNs to (1) automate the "real-bogus" classification, (2) reduce the computational costs of transient discovery. We compare the efficiency of two CNNs with similar architectures, one that uses "image triplets" (templates, search, and difference image) and one that takes as input the template and search only. We measure the decrease in efficiency associated with the loss of information in input finding that the testing accuracy is reduced from 96% to 91.1%. We further investigate how the latter model learns the required information from the template and search by exploring the saliency maps. Our work (1) confirms that CNNs are excellent models for "real-bogus" classification that rely exclusively on the imaging data and require no feature engineering task; (2) demonstrates that high-accuracy (&gt; 90%) models can be built without the need to construct difference images, but some accuracy is lost. Since once trained, neural networks can generate predictions at minimal computational costs, we argue that future implementations of this methodology could dramatically reduce the computational costs in the detection of transients in synoptic surveys like Rubin Observatory's Legacy Survey of Space and Time by bypassing the Difference Image Analysis entirely.
Metabolic Capability of a Predominant Halanaerobium sp. in Hydraulically Fractured Gas Wells and Its Implication in Pipeline Corrosion (2016)

Microbial activity associated with produced water from hydraulic fracturing operations can lead to gas souring and corrosion of carbon-steel equipment. We examined the microbial ecology of produced water and the prospective role of the prevalent microorganisms in corrosion in a gas production field in the Barnett Shale. The microbial community was mainly composed of halophilic, sulfidogenic bacteria within the order Halanaerobiales, which reflected the geochemical conditions of highly saline water containing sulfur species (S2O3 (2-), SO4 (2-), and HS(-)). A predominant, halophilic bacterium (strain DL-01) was subsequently isolated and identified as belonging to the genus Halanaerobium. The isolate could degrade guar gum, a polysaccharide polymer used in fracture fluids, to produce acetate and sulfide in a 10% NaCl medium at 37°C when thiosulfate was available. To mitigate potential deleterious effects of sulfide and acetate, a quaternary ammonium compound was found to be an efficient biocide in inhibiting the growth and metabolic activity of strain DL-01 relative to glutaraldehyde and tetrakis (hydroxymethyl) phosphonium sulfate. Collectively, our findings suggest that predominant halophiles associated with unconventional shale gas extraction could proliferate and produce sulfide and acetate from the metabolism of polysaccharides used in hydraulic fracturing fluids. These metabolic products might be returned to the surface and transported in pipelines to cause pitting corrosion in downstream infrastructure.
Fibrinogen Level as a Surrogate for the Outcome of Thrombolytic Therapy Using Tissue Plasminogen Activator for Acute Lower Extremity Intravascular Thrombosis (2013)

Fibrinogen level ≤ 150 mg/dL is associated with increased risk of major bleeding during tPA infusions. We suggest serial fibrinogen measurement as a viable method to monitor bleeding risk during lower extremity tPA infusions.
Transcriptional programs regulating seed dormancy and its release by after‐ripening in common wheat (Triticum aestivum L.) (2012)

Seed dormancy is an important agronomic trait in wheat (Trticum aestivum). Seeds can be released from a physiologically dormant state by after-ripening. To understand the molecular mechanisms underlying the role of after-ripening in conferring developmental switches from dormancy to germination in wheat seeds, we performed comparative transcriptomic analyses between dormant (D) and after-ripened (AR) seeds in both dry and imbibed states. Transcriptional activation of genes represented by a core of 22 and 435 probesets was evident in the dry and imbibed states of D seeds, respectively. Furthermore, two-way ANOVA analysis identified 36 probesets as specifically regulated by dormancy. These data suggest that biological functions associated with these genes are involved in the maintenance of seed dormancy. Expression of genes encoding protein synthesis/activity inhibitors was significantly repressed during after-ripening, leading to dormancy decay. Imbibing AR seeds led to transcriptional activation of distinct biological processes, including those related to DNA replication, nitrogen metabolism, cytoplasmic membrane-bound vesicle, jasmonate biosynthesis and cell wall modification. These after-ripening-mediated transcriptional programs appear to be regulated by epigenetic mechanisms. Clustering of our microarray data produced 16 gene clusters; dormancy-specific probesets and abscisic acid (ABA)-responsive elements were significantly overrepresented in two clusters, indicating the linkage of dormancy in wheat with that of seed sensitivity to ABA. The role of ABA signalling in regulating wheat seed dormancy was further supported by the down-regulation of ABA response-related probesets in AR seeds and absence of differential expression of ABA metabolic genes between D and AR seeds.
Next-Generation Antibody Therapeutics: Discovery, Development and Beyond: highlights of the third annual conference of the Chinese Antibody Society (2019)

The Chinese Antibody Society (CAS) convened the third annual conference in Cambridge, Massachusetts, USA on April 7, 2019. More than 600 global members attended the meeting. The theme of this conference was Next-Generation Antibody Therapeutics: Discovery, Development and Beyond. The meeting covered a vast variety of topics including cancer immunotherapy, single-domain antibodies as well as bispecific antibodies, immunotoxins, transgenic mouse platforms for next-generation monoclonal antibody discovery and antibody chemistry, manufacturing and controls (CMCs). Two hot topics were comprehensively discussed by the prestigious panelists and hosts at the panel discussions during the conferences, i.e., bispecific antibodies and antibody CMC.
Facile Crystallization of Ice Ih via Formaldehyde Hydrate in Ultrahigh Vacuum under Cryogenic Conditions (2021)

Although hexagonal ice (ice Ih) is the most common and highly studied crystalline form of ice, its nucleation from clathrate hydrates is poorly understood. Here, we report the formation of ice Ih through the dissociation of formaldehyde hydrate, prepared under ultrahigh vacuum (UHV) in the temperature window of 130–135 K. This unique route for crystallization is highly facile, and it occurs below the usual crystallization temperature of ice Ih of 155 K in UHV; the associated activation energy is also lower. Time-dependent reflection absorption infrared spectroscopy was used to detect the formaldehyde hydrate and to determine the crystallization kinetics of ice Ih. The dissociation of formaldehyde hydrate is found to be a diffusion-controlled process, which reduces the activation barrier of crystallization. This study provides evidence that formaldehyde hydrate can exist in extremely low (P, T) conditions without forming the geminal diol or its polymer in the presence of water. This new and facile route of crystallization in the context of interstellar environments may have implications for cometary and prebiotic science.
Neutralizing IgG at the Portal of Infection Mediates Protection against Vaginal Simian/Human Immunodeficiency Virus Challenge (2013)

Neutralizing antibodies may have critical importance in immunity against human immunodeficiency virus type 1 (HIV-1) infection. However, the amount of protective antibody needed at mucosal surfaces has not been fully established. Here, we evaluated systemic and mucosal pharmacokinetics (PK) and pharmacodynamics (PD) of 2F5 IgG and 2F5 Fab fragments with respect to protection against vaginal challenge with simian-human immunodeficiency virus-BaL in macaques. Antibody assessment demonstrated that 2F5 IgG was more potent than polymeric forms (IgM and IgA) across a range of cellular and tissue models. Vaginal challenge studies demonstrated a dose-dependent protection for 2F5 IgG and no protection with 2F5 Fab despite higher vaginal Fab levels at the time of challenge. Animals receiving 50 or 25 mg/kg of body weight 2F5 IgG were completely protected, while 3/5 animals receiving 5 mg/kg were protected. In the control animals, infection was established by a minimum of 1 to 4 transmitted/founder (T/F) variants, similar to natural human infection by this mucosal route; in the two infected animals that had received 5 mg 2F5 IgG, infection was established by a single T/F variant. Serum levels of 2F5 IgG were more predictive of sterilizing protection than measured vaginal levels. Fc-mediated antiviral activity did not appear to influence infection of primary target cells in cervical explants. However, PK studies highlighted the importance of the Fc portion in tissue biodistribution. Data presented in this study may be important in modeling serum levels of neutralizing antibodies that need to be achieved by either vaccination or passive infusion to prevent mucosal acquisition of HIV-1 infection in humans.
Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Analysis of DNA on Microarrays (2006)

This procedure offers an operational short-cut compared with standard MALDI procedures for preparation of oligonucleotides, including purification, and thus is an efficient tool for genotyping applications, particularly those requiring accurate, flexible, and rapid data generation and medium throughput.
ChemInform Abstract: Stereoselective Syntheses of α‐Hydroxy‐γ‐amino Acids: Possible γ‐Turn Mimetics. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Tunable tapered waveguide for efficient compression of light to graphene surface plasmons (2016)

Dielectric-graphene-dielectric (DGD) structure has been widely used to construct optical devices at infrared region with features of small footprint and low-energy dissipation. The optical properties of graphene can be manipulated by changing its chemical potential by applying a biased voltage onto graphene. However, the excitation efficiency of surface wave on graphene by end-fire method is very low because of large wavevector mismatch between infrared light and surface wave. In this paper, a dielectric-semiconductor-dielectric (DSD) tapered waveguide with magnetic tunability for efficient excitation of surface waves on DGD at infrared region is proposed and analyzed. Efficient excitation of surface waves on DGD with various chemical potentials in graphene layer and incident frequencies can be attained by merely changing the external magnetic field applied onto the DSD tapered waveguide. The electromagnetic simulations verify the design of the proposed structure. More importantly, the constituent materials used in the proposed structure are available in nature. This work opens the door toward various applications in the field of using surface waves.
Experimental Infection of Pregnant Cattle with Bluetongue Virus Serotype 11 between Postbreeding Days 21 and 48 (1993)

Four bluetongue virus (BTV)-seronegative heifers and 2 BTV-seropositive heifers were inoculated with the virulent strain UC-8 of BTV-11 between postbreeding days (PBD) 21 and 30. The heifers were observed for 10-18 days after inoculation for clinical signs, and pregnancy was monitored by ultrasound examination of the uterus and by plasma progesterone levels. Blood samples were collected daily after inoculation and processed for virus isolation and titration. Heifers were euthanized between PBD 31 and PBD 48, and tissues were collected for virologic and pathologic examination. All but 1 heifer inoculated on PBD 21 remained pregnant after BTV inoculation. A cystic corpus luteum was found in the ovary of the nonpregnant heifer, but BTV was not isolated from the reproductive tract of this heifer. Three of the inoculated heifers that remained pregnant showed mild multifocal areas of perivascular lymphocytic infiltration in the ovary. BTV was reisolated from spleen and prescapular and peribronchial lymph nodes 10 days after inoculation from 3 of the 4 BTV-seronegative heifers. BTV was also reisolated from the uterus of 1 of the heifers that remained pregnant, but microscopic lesions were not found in this organ.
Cognitive computing building block: A versatile and efficient digital neuron model for neurosynaptic cores (2013)

Marching along the DARPA SyNAPSE roadmap, IBM unveils a trilogy of innovations towards the TrueNorth cognitive computing system inspired by the brain's function and efficiency. Judiciously balancing the dual objectives of functional capability and implementation/operational cost, we develop a simple, digital, reconfigurable, versatile spiking neuron model that supports one-to-one equivalence between hardware and simulation and is implementable using only 1272 ASIC gates. Starting with the classic leaky integrate-and-fire neuron, we add: (a) configurable and reproducible stochasticity to the input, the state, and the output; (b) four leak modes that bias the internal state dynamics; (c) deterministic and stochastic thresholds; and (d) six reset modes for rich finite-state behavior. The model supports a wide variety of computational functions and neural codes. We capture 50+ neuron behaviors in a library for hierarchical composition of complex computations and behaviors. Although designed with cognitive algorithms and applications in mind, serendipitously, the neuron model can qualitatively replicate the 20 biologically-relevant behaviors of a dynamical neuron model.
Synthesis, Characterization, and Simulation of Four-Armed Megamolecules (2021)

This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a <i>para</i>-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.
Pten Loss and RAS/MAPK Activation Cooperate to Promote EMT and Metastasis Initiated from Prostate Cancer Stem/Progenitor Cells (2012)

PTEN loss or PI3K/AKT signaling pathway activation correlates with human prostate cancer progression and metastasis. However, in preclinical murine models, deletion of Pten alone fails to mimic the significant metastatic burden that frequently accompanies the end stage of human disease. To identify additional pathway alterations that cooperate with PTEN loss in prostate cancer progression, we surveyed human prostate cancer tissue microarrays and found that the RAS/MAPK pathway is significantly elevated in both primary and metastatic lesions. In an attempt to model this event, we crossed conditional activatable K-ras(G12D/WT) mice with the prostate conditional Pten deletion model. Although RAS activation alone cannot initiate prostate cancer development, it significantly accelerated progression caused by PTEN loss, accompanied by epithelial-to-mesenchymal transition (EMT) and macrometastasis with 100% penetrance. A novel stem/progenitor subpopulation with mesenchymal characteristics was isolated from the compound mutant prostates, which was highly metastatic upon orthotopic transplantation. Importantly, inhibition of RAS/MAPK signaling by PD325901, a mitogen-activated protein (MAP)-extracellular signal-regulated (ER) kinase (MEK) inhibitor, significantly reduced the metastatic progression initiated from transplanted stem/progenitor cells. Collectively, our findings indicate that activation of RAS/MAPK signaling serves as a potentiating second hit to alteration of the PTEN/PI3K/AKT axis, and cotargeting both the pathways is highly effective in preventing the development of metastatic prostate cancers.
Supplementary Figure 1 from Enhanced Cancer Radiotherapy through Immunosuppressive Stromal Cell Destruction in Tumors (2023)

&lt;p&gt;PDF file - 1324K, Schematic diagram of the potential mechanisms of immune mediated antitumor effects as a result of intratumor peptide delivery following radiation.&lt;/p&gt;
Influence of Donor Pretreatment with Dopamine on Allogeneic Kidney Transplantation after Prolonged Cold Storage in Rats (2005)

Pretreatment of organ donors with dopamine improves short- and long-term outcome after prolonged cold storage and subsequent allogeneic kidney transplantation in rats. The authors' experimental data demonstrate that donor treatment is a simple and effective approach for preventing long-term graft loss after kidney transplantation.
ChemInform Abstract: Metal Complex Catalyzed Reactions (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.