gebhart/patrepeval huggingface dataset:
RACER: Bit-Pipelined Processing Using Resistive Memory (2021)

To combat the high energy costs of moving data between main memory and the CPU, recent works have proposed to perform processing-using-memory (PUM), a type of processing-in-memory where operations are performed on data in situ (i.e., right at the memory cells holding the data). Several common and emerging memory technologies offer the ability to perform bitwise Boolean primitive functions by having interconnected cells interact with each other, eliminating the need to use discrete CMOS compute units for several common operations. Recent PUM architectures extend upon these Boolean primitives to perform bit-serial computation using memory. Unfortunately, several practical limitations of the underlying memory devices restrict how large emerging memory arrays can be, which hinders the ability of conventional bit-serial computation approaches to deliver high performance in addition to large energy savings.
Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection (2020)

Extensive Recombination and Strong Purifying Selection among coronaviruses from different hosts facilitate the emergence of SARS-CoV-2.
Assessment of Lower Urinary Tract Functional Deficit in Rats With Contusive Spinal Cord Injury (1998)

Traumatic spinal cord injury (SCI) produces lower urinary tract (LUT) dysfunction that has been studied in surgical transection models. Our aim was to assess LUT functional deficit in a clinically relevant model of incomplete SCI to investigate how partial preservation of supraspinal connections might affect LUT dysfunction. Standardized weight-drop contusion (10 g x 2.5 cm) or complete transection, was produced at T8 in female Sprague-Dawley rats. Behavioral tests were used to assess hind limb sensorimotor function at Day 1 after surgery and weekly thereafter. The urometric experiments were conducted on groups (n = 7) of uninjured rats and on injured rats during Weeks 1 and 2 after SCI (before and after spontaneous voiding was established) as well as Week 2 after a complete transection (n = 3). Under anesthesia, the bladder was continuously perfused with saline. Changes in bladder pressure and external urethral sphincter (EUS) electrical activity were monitored. The bladder was then dissected and weighed and both the bladder and spinal cord were fixed for pathoanatomical analyses. Our results indicate that several aspects of LUT dysfunction after contusive SCI were similar to transection, e.g., reduction of voiding efficiency (approximately 5% of normal value), decrease in inter-contraction interval (47%), increase in bladder capacity (8-fold), and weight (4.6-fold). One aspect appeared different from transection--partial recovery from acute bladder/sphincter dyssynergia. Because the coordination of bladder and EUS function is mediated by brainstem pathways, partial recovery of synergy after SCI was likely due to sparing of some relevant bulbospinal projections as was confirmed by retrograde transneuronal viral tracing.
Measuring the reusability of test collections (2010)

While test collection construction is a time-consuming and expensive process, the true cost is amortized by reusing the collection over hundreds or thousands of experiments. Some of these experiments may involve systems that retrieve documents not judged during the initial construction phase, and some of these systems may be "hard" to evaluate: depending on which judgments are missing and which judged documents were retrieved, the experimenter's confidence in an evaluation could potentially be very low. We propose two methods for quantifying the reusability of a test collection for evaluating new systems. The proposed methods provide simple yet highly effective tests for determining whether an existing set of judgments is useful for evaluating a new system. Empirical evaluations using TREC datasets confirm the usefulness of our proposed reusability measures. In particular, we show that our methods can reliably estimate confidence intervals that are indicative of collection reusability.
Signaling in the phytomicrobiome: breadth and potential (2015)

Higher plants have evolved intimate, complex, subtle, and relatively constant relationships with a suite of microbes, the phytomicrobiome. Over the last few decades we have learned that plants and microbes can use molecular signals to communicate. This is well-established for the legume-rhizobia nitrogen-fixing symbiosis, and reasonably elucidated for mycorrhizal associations. Bacteria within the phytomircobiome communicate among themselves through quorum sensing and other mechanisms. Plants also detect materials produced by potential pathogens and activate pathogen-response systems. This intercommunication dictates aspects of plant development, architecture, and productivity. Understanding this signaling via biochemical, genomics, proteomics, and metabolomic studies has added valuable knowledge regarding development of effective, low-cost, eco-friendly crop inputs that reduce fossil fuel intense inputs. This knowledge underpins phytomicrobiome engineering: manipulating the beneficial consortia that manufacture signals/products that improve the ability of the plant-phytomicrobiome community to deal with various soil and climatic conditions, leading to enhanced overall crop plant productivity.
MOVPE growth and characterization of Ga(NAsP) laser structures monolithically integrated on Si (001) substrates (2010)

In this work we focus on the MOVPE growth of Ga(NAsP) laser structures for electrical current injection lattice matched on exactly orientated Si substrates and their structural characterization.
CXCR6 regulates localization of tissue-resident memory CD8 T cells to the airways (2019)

Resident memory T cells (T<sub>RM</sub> cells) are an important first-line defense against respiratory pathogens, but the unique contributions of lung T<sub>RM</sub> cell populations to protective immunity and the factors that govern their localization to different compartments of the lung are not well understood. Here, we show that airway and interstitial T<sub>RM</sub> cells have distinct effector functions and that CXCR6 controls the partitioning of T<sub>RM</sub> cells within the lung by recruiting CD8 T<sub>RM</sub> cells to the airways. The absence of CXCR6 significantly decreases airway CD8 T<sub>RM</sub> cells due to altered trafficking of CXCR6<sup>-/-</sup> cells within the lung, and not decreased survival in the airways. CXCL16, the ligand for CXCR6, is localized primarily at the respiratory epithelium, and mice lacking CXCL16 also had decreased CD8 T<sub>RM</sub> cells in the airways. Finally, blocking CXCL16 inhibited the steady-state maintenance of airway T<sub>RM</sub> cells. Thus, the CXCR6/CXCL16 signaling axis controls the localization of T<sub>RM</sub> cells to different compartments of the lung and maintains airway T<sub>RM</sub> cells.
Novel therapeutic uses and formulations of botulinum neurotoxins: a patent review (2012 – 2014) (2015)

The clinical and commercial success of BoNTs has prompted investigation into novel BoNTs or BoNT-mediated chimeras with promising in vitro results. Distinct strategies including the use of nanoformulations and targeted delivery have been implemented to identify new indication and improved functionality. Greater understanding of their systemic exposure, efficacy and safety profiles will be required for further development.
Proceedings of the eighth ACM SIGKDD international conference on Knowledge discovery and data mining (2002)

The KDD 2002 conference, held from 23rd to 26th July 2002, was the eighth in the series. It represented a return to the country in which the series was launched: the first was held in Montreal, Canada, and this, the eighth, was held in Edmonton, Canada. In the years between the first conference in the series and this present one, data mining has be, come a well-established discipline. It has continued to strengthen its links to other data analytic disciplines, including statistics, machine learning, pattern recognition, visualization, and database technology, but has now clearly carved out a niche of its own. Over the period in which this series has been running, hardware technology has continued to advance in great leaps, with the result that large databases have continued to grow in both number and size. The implication is that the challenge of data mining is even more important, that the problems requiring data mining solutions are ever more ubiquitous, and that new tools and methods for tackling are even more necessary.KDD 2002 received a record number of submitted papers - 307 in total, 37 of which were considered for the industral/applicafion track. Among the 270 research submissions, 32 were selected (12%) for full papers; and among the 37 industrial/application submissions, 12 (32%) were selected for full papers. An additional 44 submissions were chosen to be presented as posters, a vast majority of which were research submissions. This low rate of acceptance reflects a conscious effort to maintain the very high standards of quality and relevance, which have been achieved by previous conferences in the series. It means that the papers and posters in the proceedings represent the cutting edge of data mining problemsl solutions, and technology. On the other hand, this policy inevitably meant that many excellent contributions did not make it to the final program. The choice had to be informed by balance as well as quality - KDD 2002 had to showcase research in data mining across the entire frontier of the discipline. This breadth was reflected in the choice of invited speakers, both well known in the data mining; community, but from different backgrounds: Daryl Pregibon and Geoff Hinton. The program also includes 6 workshops in such diverse areas as 'Data Mining in Bioinformatics', 'Web Mining', 'Multimedia Data Mining', 'Multi-Relational Data Mining', 'Temporal Data Mining', and 'Fractals in Data Mining' as well as 6 tutorials on 'Text Mining for Bioinformatics', 'Querying and Mining Data Streams', 'Link Analysis', 'Multivariate Density Estimation', 'Common Reasons Data Mining Projects Fail', and 'Visual Data Mining'.
Identification of a bona fide microRNA biomarker in serum exosomes that predicts hepatocellular carcinoma recurrence after liver transplantation (2015)

Circulating miRs in serum exosomes have potential as novel biomarkers for predicting HCC recurrence.
Can AI accommodate imagistic expertise? (2002)

After years of focussing almost exclusively on rather primitive symbolic forms of knowledge representation, AI has started a systematic attempt to design and implement a computational correlate to human diagrammatic representation and reasoning. However, a number of thinkers are on record as confidently claiming that such representation and reasoning is forever beyond a digital computer. Are such claims to be taken seriously? We think so/spl minus/when they are based on mental imagery more sophisticated than that which AI customarily concerns itself with. This "recalcitrant" imagery is the province of certain experts (e.g. authors and screenwriters).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bipolar Membrane Design for Hybrid PEM/AEM Fuel Cells (2016)

Bipolar membranes fuel cells utilizing both anion and cation conductive materials have several advantages compared to their purely acidic or alkaline counterparts. The potential advantages include improved water management through self-hydration and facile electrode kinetics. Material transport properties play an important role in determining viability of membrane and ionomer materials. In addition, the cation-anion junction itself is a critical element in determining device performance because it must be sufficiently conductive to ionic species and mechanically stable to withstand the internal pressure from water formation. A series of electrochemical devices using different bipolar membranes have been fabricated for use in direct methanol and hydrogen fuel cells. This study examines both single- and two-membrane systems containing cation-anion junctions. These fuel cells were characterized by performance metrics and electrochemical impedance spectroscopy to determine specific areas for improvement in the bipolar devices. Operation under varying humidity was studied in order to understand water management necessary for bipolar fuel cells. These results will be used in the future optimization of bipolar devices. Financial support from US Office of the Deputy Assistant Secretary of the Army for Defense Exports and Cooperation (DASA-DE&amp;C) is gratefully acknowledged.
Sodium dodecyl sulfate and sodium dodecyl benzenesulfonate are ligands for peroxisome proliferator-activated receptor γ (2013)

Sodium dodecyl sulfate (SDS) and sodium dodecyl benzenesulfonate (SDBS) are widely used anionic surfactants in household, industrial, and institutional cleaners. Although there are many reports of their toxic effects, few studies have focused on the pharmacological properties of these surfactants. Peroxisome proliferator-activated receptor (PPAR) γ is a transcriptional factor belonging to the nuclear receptor superfamily. The ligands of PPARγ regulate its transcriptional activity and modulate many biological functions, including adipocyte differentiation and lipid metabolism. In this study, we investigated the ligand activities of SDS and SDBS for nuclear receptors using time-resolved fluorescence resonance energy transfer-based coactivator recruitment assays. SDS and SDBS showed selective ligand activities for PPARγ and these ligand activities were eliminated by a PPARγ antagonist. SDS and SDBS also promoted adipocyte differentiation accompanied by upregulation of adipocyte-specific gene expression in 3T3-L1 preadipocytes. These findings reveal novel actions of anionic alkyl surfactants as PPARγ ligands.
On a new incentive and market based framework for multi-tier shared spectrum access systems (2014)

The popularity of the smartphone and the resulting increase in the volume of wireless data traffic has created a large gap between bandwidth supply and demand. An attractive and less expensive solution to re-farming of spectrum is to maximize the use of under-utilized bands through spectrum sharing. Recent efforts in this area, that propose operation of wireless systems in shared spectrum, address the main challenge of how shared spectrum access systems can efficiently share and utilize spectrum resources. In this paper, we focus on the framework for multi-tier shared spectrum operation in wireless networks, where multiple entities - the Shared Spectrum Managers (SSMs) - dynamically acquire, manage and sell shared spectrum. We derive an auction based spectrum resource assignment algorithm which maximizes the overall system efficiency and provides incentives to the incumbents to make spectrum available for sharing. We demonstrate that the algorithm can be implemented in practice through messaging in which the SSM dynamically negotiates spectrum bidding and asking prices with the shared spectrum users. Simulations are performed under different scenarios and assumptions both to verify that the algorithm achieves the maximum utility value for shared spectrum systems, and to compare the outcome behavior under each scenario. Based on the observations, potential regulations that would need to be put in place in each scenario are discussed, and a set of future development areas are identified based on these observations.
Homeoprotein neuroprotection of embryonic neuronal cells (2019)

ABSTRACT Most homeoprotein transcription factors have a highly conserved internalization domain used in intercellular transfer. Internalization of homeoproteins ENGRAILED1 or ENGRAILED2 promotes the survival of adult dopaminergic cells, whereas that of OTX2 protects adult retinal ganglion cells. Here we characterize the in vitro neuroprotective activity of several homeoproteins in response to H 2 O 2 . Protection is observed with ENGRAILED1, ENGRAILED2, OTX2, GBX2 and LHX9 on midbrain and striatal embryonic neurons whereas cell-permeable c-MYC shows no protective effects. Therefore, five homeoproteins belonging to 3 different classes (ANTENNAPEDIA, PAIRED and LIM) share the ability to protect embryonic neurons from midbrain and striatum. Because midbrain and striatal neurons do not express the same repertoire of the 4 proteins, a lack of neuronal specificity together with a general protective activity can be proposed. In contrast, hEN1 and GBX2 exerted no protection on non-neuronal cells including mouse embryo fibroblasts, macrophages or HeLa cells. For the 4 proteins, protection against cell-death correlated with a reduction in the number of H 2 O 2 -induced DNA break foci in midbrain and striatal neurons. In conclusion, within the limit of the number of cell types and homeoproteins tested, homeoprotein protection against oxidative stress-induced DNA breaks and death is specific to neurons but shows no homeoprotein or neuronal type specificity. SIGNIFICANCE STATEMENT Homeoproteins are DNA binding proteins regulating gene expression throughout life. Many of them transfer between cells and are thus internalized by live cells. This has allowed for their use as therapeutic proteins in animal models of Parkinson disease and glaucoma. Part of their therapeutic activity is through a protection against neuronal death. Here we show that internalized homeoproteins from three different classes protect embryonic ventral midbrain and striatal neurons from oxidative stress, both at the level of DNA damage and survival. The interest of this finding is that it lends weight to the possibility that many homeoproteins play a role in neuroprotection through shared mechanisms involving, in particular, DNA protection against stress-induced breaks.
Ion trap for mass-selective production of nanoclusters (1997)

To form nanoclusters with a specified atomic structure, an electrical trapping technique of charged particles was developed that allows us to confine, grow, and mass selectively eject cluster ions. Theoretical calculations and experiments using inert gas ions indicate that the developed ion trap can confine ions with a wide range of mass values using the external field of an ac quadrupole, and send out the ions mass selectively through the internal region of the quadrupole. To demonstrate performance, Si6H12+ clusters were selectively grown using SiH4 as a starting material. In the trap, confined SiHx+ ions were allowed to react with neutral SiH4 molecules or SiHy radicals, and SinHx+ clusters were grown, from which Si6H12+ clusters were automatically ejected by tuning trapping parameters.
Laser Ablation of Poly(methylmethacrylate) Doped with Aromatic Compounds: Laser Intensity Dependence of Absorption Coefficient (1999)

We developed a novel method of obtaining an absorption coefficient which depends on the laser intensity, since a single-photon absorption coefficient of a polymer could not be applied to laser ablation. The relationship between the nonlinear absorption coefficient and the laser intensity was derived from experimental data of transmission and incident laser intensities. Using the nonlinear absorption coefficient of poly(methylmethacrylate) doped with benzil and pyrene, we succeeded in fitting the relationship of etch depth and laser intensity, obtained experimentally, and discussed the energy absorbed by the polymer at the threshold fluence.
The absence of BBSome function decreases synaptogenesis and causes ectopic synapse formation in the retina (2020)

Photoreceptors possess ribbon synapses distinct from the conventional synapses in the brain. Little is known about the function of the BBSome, a complex integral in ciliary and intracellular trafficking, in ribbon synaptic formation. We performed immunohistochemistry using retinas from Bardet-Biedl Syndrome (BBS) mouse models and found that BBS mutant animals have significantly fewer ribbon synapses in the outer plexiform layer and increased ectopic synapses in the outer nuclear layer compared to controls. Many ectopic synapses in BBS mutant retinas are associated with horizontal cell axonal processes that aberrantly intrude into the outer nuclear layer. To determine whether this horizontal cell phenotype is a consequence of retinal degeneration, we examined this phenotype in mice with photoreceptor-specific inactivation of the BBSome induced by Cre recombinase driven by the rhodopsin promoter. At three months of age, despite retinal degeneration, Bbs8<sup>floxed/floxed</sup>; Rho-Cre<sup>+</sup> mice lack the aberrant intrusion of horizontal cell processes. At 6 months, some horizontal cell processes intrude into the outer nuclear layer in Bbs8<sup>floxed/floxed</sup>; Rho-Cre<sup>+</sup> mice, but the phenotype does not recapitulate the phenotypic severity observed in young congenital BBS mutant mice. Therefore, the lack of BBSome function negatively impacts retinal synaptogenesis, and causes horizontal cell defects in a potentially cell-autonomous fashion.
Efficient estimation of 3D Euclidean distance fields from 2D range images (2003)

Several existing algorithms for reconstructing 3D models from range data first approximate the object's 3D distance field to provide an implicit representation of the scanned object and then construct a surface model of the object using this distance field. In these existing approaches, computing and storing 3D distance values from range data contribute significantly to the computational and storage requirements. This paper presents an efficient method for estimating the 3D Euclidean distance field from 2D range images that can be used by any of these algorithms. The proposed method uses Adaptively Sampled Distance Fields to minimize the number of distance evaluations and significantly reduce storage requirements of the sampled distance field. The method is fast because much of the computation required to convert the line-of-sight range distances to Euclidean distances can be done during a pre-processing step in the 2D coordinate space of each range image.
Specific suppression elicited by EL4 lymphoma cells in syngeneic mice. Specificity includes self‐antigens on EL4 (1987)

In vivo, subclones derived from EL4 lymphoma cells generate suppressor T lymphocytes specific for anti-EL4 immune responses. Spleen cells of EL4-sensitized C57BL/6 mice down-regulate the in vitro induction of EL4-specific cytolytic T lymphocytes (CTL). In addition, EL4-sensitized spleen cells interfere with the antigen response of two T lymphocyte clones. These recognize, in an H-2b context, a self-antigen on spleen cells that is also expressed by transformed cells, including EL4. The simultaneous anti-self and anti-EL4 specificity of the helper and suppressor activities suggests, therefore, that they are the product of an in vivo autoimmune reaction to EL4. The anti-self suppression might aim to re-establish self-tolerance, at the same time down-regulating responses against immunogenic epitopes that are co-expressed with the self-antigen on the EL4 cells. This agrees well with our observation that suppressor T cells, apparently elicited by suppressogenic epitopes on non-immunogenic EL4 subclones, down-regulate the CTL response elicited by immunogenic EL4 subclones. The additional self-specificity of this suppression indicates that the suppressogenic epitopes at least in part represent EL4 self-antigens.