gebhart/patrepeval huggingface dataset:
FAULT DIAGNOSIS IN DESIGNSWITH CONVOLUTIONAL COMPACTORS (2004)

The paper introduces a new non-adaptive fault diagnosis technique for scan-based designs. The proposed scheme guarantees accurate and time-efficient identification of failing scan cells based on results of a convolutional test response compaction.
The Tissue Plasminogen Activator (Tpa/Plasmin) Extracellular Proteolytic System Regulates Seizure-Induced Hippocampal Mossy Fiber Outgrowth through a Proteoglycan Substrate (2000)

Short seizure episodes are associated with remodeling of neuronal connections. One region where such reorganization occurs is the hippocampus, and in particular, the mossy fiber pathway. Using genetic and pharmacological approaches, we show here a critical role in vivo for tissue plasminogen activator (tPA), an extracellular protease that converts plasminogen to plasmin, to induce mossy fiber sprouting. We identify DSD-1-PG/phosphacan, an extracellular matrix component associated with neurite reorganization, as a physiological target of plasmin. Mice lacking tPA displayed decreased mossy fiber outgrowth and an aberrant band at the border of the supragranular region of the dentate gyrus that coincides with the deposition of unprocessed DSD-1-PG/phosphacan and excessive Timm-positive, mossy fiber termini. Plasminogen-deficient mice also exhibit the laminar band and DSD- 1-PG/phosphacan deposition, but mossy fiber outgrowth through the supragranular region is normal. These results demonstrate that tPA functions acutely, both through and independently of plasmin, to mediate mossy fiber reorganization.
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing (2022)

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.
Performance-constrained pipelining of software loops onto reconfigurable hardware (2002)

Retiming and slowdown are algorithms that can be used to pipeline synchronous circuits. Iterative modulo scheduling is an algorithm for software pipelining in the presence of resource constraints. Integrating the best features of both yields a pipelining algorithm, retimed modulo scheduling, that can more effectively exploit the idiosyncrasies of reconfigurable hardware. It also fits naturally into a design space exploration process to trade-off speed for power, energy or area.
Toll like Receptor 2 Signaling Regulates Hematopoietic Stem Cell Function and Promotes G-CSF Mediated HSC Mobilization (2014)

Abstract Toll like receptors (TLRs) are a family of pattern recognition receptors that play a central role in pathogen recognition and shaping the innate immune response. While most of the studies of the role of TLRs have focused on mature immune cell populations, recent reports suggest that TLR signaling may regulate the immune response from the level of the hematopoietic stem cell (HSC). In this study, we sought to further elucidate the effects of systemic TLR ligand exposure on HSCs and determine the cell-intrinsic versus extrinsic effects of such exposure. We specifically focused on TLR2 signaling, as although TLR2 is expressed on HSCs, it’s role in their regulation is not clear. Furthermore, enhanced TLR2 signaling is associated with myelodysplastic syndrome (Wei et al, Leukemia 2013), suggesting that aberrant signaling through this receptor may have clinically significant effects on HSC function. To elucidate the role of TLR2 signaling in regulating HSCs, we used mice with genetic loss of TLR2, as well as a synthetic agonist of TLR2 (PAM3CSK4) to determine the effects of TLR2 signaling loss or gain, respectively, on HSC cycling, mobilization and function. While TLR2 expression is not required for normal HSC function, treatment of wild-type mice with PAM3CSK4 leads to expansion of HSCs in the bone marrow and spleen, increased HSC cycling, and loss of HSC function in competitive bone marrow transplantation experiments. As TLR2 is expressed on a variety of stromal and hematopoietic cell types, we used bone marrow chimeras (Tlr2-/- + Tlr2+/+ marrow transplanted into Tlr2+/+ recipients) to determine if the effects of PAM3CSK4 treatment are cell intrinsic or extrinsic. The data suggests that HSC cycling and expansion in the marrow and spleen upon PAM3CSK4 treatment are extrinsic (occurring in both transplanted HSC populations), and are associated with increased serum levels of G-CSF. Indeed, inhibition of G-CSF using either a neutralizing antibody or mice lacking the G-CSF receptor (Csf3r-/-) leads to even further enhanced HSC bone marrow expansion upon G-CSF treatment but significantly reduced numbers of spleen HSCs compared to similarly treated wild-type mice. This suggests mobilization in response to TLR2 signaling is an indirect, G-CSF-mediated process. Ongoing studies are aimed at determining the contribution of G-CSF to the PAM3CSK4- induced loss of HSC function, and determining the source (stromal vs hematopoietic) of G-CSF production upon PAM3CSK4 exposure. Collectively, this data suggest that TLR2 signaling affects HSCs in a largely extrinsic fashion, with G-CSF playing a major role in regulating the effects of TLR2 ligand exposure on HSCs. Disclosures No relevant conflicts of interest to declare.
GENE-14. UNIQUE MOLECULAR AND CLINICAL FEATURES OF LI-FRAUMENI SYNDROME ASSOCIATED BRAIN TUMOURS (2019)

Li-Fraumeni syndrome (LFS) is a condition characterized by germ-line TP53 mutation and predisposition to various types of malignant neoplasms in childhood. We aimed to characterize spectrum of brain tumours in children associated with LFS. We gathered clinical information on LFS patients treated since 1990 at our department. Where the tissue was available, we performed molecular analysis consisting of whole genome methylation array and/or sequencing. We identified 15 LFS patients diagnosed with brain tumours; six with choroid plexus carcinoma (CPC), four with glioma, three with medulloblastoma, one PNET and one spinal myxopapilary ependymoma. Twelve of these patients presented with brain tumour as their first malignancy. Two patients were previously treated for rhabdomyosarcoma and developed glioma in radiation field. One patient was diagnosed with medulloblastoma after adrenocortical carcinoma. Out of six patients with CPC, three are alive, with two treated with radiation therapy. Gliomas consisted of three diffuse astrocytomas (DA) and one glioblastoma. DAs were diagnosed at later age (14 to 18 years) and molecularly characterized by rare IDH1 R132G mutation. One glioblastoma was classified as GBM_other using NMP2.0. All four patients are alive with median 4 years from diagnosis of glioma, including the patient with glioblastoma. All medulloblastomas were SHH group with tumor location in the cerebellar hemisphere. Two patients treated with combined radiation and chemotherapy died of secondary malignancy 4 and 5 years from the primary diagnosis. Last patient is currently being treated with radiation sparing approach. In our cohort, majority of patients developed brain tumour as their first malignancy. Radiation sparing approaches need to be implemented to decrease risks of secondary cancers. Gliomas and medulloblastomas seem to harbour distinct molecular features compared to their sporadic counterparts.
Simple Hydrogen Plasma Doping Process of Amorphous Indium Gallium Zinc Oxide-Based Phototransistors for Visible Light Detection (2018)

A homojunction-structured amorphous indium gallium zinc oxide (a-IGZO) phototransistor that can detect visible light is reported. The key element of this technology is an absorption layer composed of hydrogen-doped a-IGZO. This absorption layer is fabricated by simple hydrogen plasma doping, and subgap states are induced by increasing the amount of hydrogen impurities. These subgap states, which lead to a higher number of photoexcited carriers and aggravate the instability under negative bias illumination stress, enabled the detection of a wide range of visible light (400–700 nm). The optimal condition of the hydrogen-doped absorption layer (HAL) is fabricated at a hydrogen partial pressure ratio of 2%. As a result, the optimized a-IGZO phototransistor with the HAL exhibits a high photoresponsivity of 1932.6 A/W, a photosensitivity of 3.85 × 106, and a detectivity of 6.93 × 1011 Jones under 635 nm light illumination.
Material characterization using a millimeter wave portal-based imaging system for security screening (2013)

The following contribution presents two methodologies to obtain geometry and constitutive parameters information about low permittivity lossless dielectric materials using an existing portal-based mm-wave imaging setup. While characterization of high permittivity dielectrics is relatively affordable in SAR images, the low amount of power reflected back by low permittivity bodies makes their characterization a challenging task. The first technique makes use of normal and 45° illumination angles to overcome the permittivity-geometry uncertainty appearing on each independent case. Second method takes advantage of the relationship between reflection coefficient amplitudes between two media, which can be directly extracted from the SAR image to provide an estimation of the dielectric object permittivity. Uncertainty associated to every technique can be reduced by properly combining them. A simulation-based application example is presented for validation purposes.
Can we predict the severe course of COVID-19 - a systematic review and meta-analysis of indicators of clinical outcome? (2021)

This comprehensive meta-analysis found age, cerebrovascular disease, CRP, LDH and cTnI to be the most important risk-factors that predict severe COVID-19 outcomes and will inform clinical scores to support early decision-making.
Solar Thermal Production of H2 Using Fe2O3-YSZ Materials. (2008)

Abstract not provided.
Cyclophilin inhibitors for the treatment of HCV infection. (2010)

Cyclophilins (Cyps) constitute one of the three families of peptidyl prolyl isomerase enzymes. CypA is the prototypical member of the Cyp family and is the predominant Cyp expressed in human cells. Recent studies indicate that CypA has an essential role in supporting HCV-specific RNA replication and protein expression. CypA interacts with several virally expressed proteins, including the non-structural (NS) proteins NS2, NS5A and NS5B, and may regulate diverse activities ranging from polypeptide processing to viral assembly. The introduction of non-immunosuppressive Cyp inhibitors into clinical trials confirms that Cyp inhibition is a valid strategy for developing novel therapeutics for the treatment of chronic HCV infection. This review describes the cyclophilin protein family and the potential roles played by cyclophilins in supporting HCV RNA replication and protein expression, as well as the initial clinical results obtained with a novel series of non-immunosuppressive cyclophilin inhibitors that established the clinical proof of concept for this emerging class of therapeutic agents.
Radiative heat transfer and nonequilibrium Casimir-Lifshitz force in many-body systems with planar geometry (2017)

A general theory of photon-mediated energy and momentum transfer in $N$-body planar systems out of thermal equilibrium is introduced. It is based on the combination of the scattering theory and the fluctuational-electrodynamics approach in many-body systems. By making a Landauer-like formulation of the heat transfer problem, explicit formulas for the energy transmission coefficients between two distinct slabs as well as the self-coupling coefficients are derived and expressed in terms of the reflection and transmission coefficients of the single bodies. We also show how to calculate local equilibrium temperatures in such systems. An analogous formulation is introduced to quantify momentum transfer coefficients describing Casimir-Lifshitz forces out of thermal equilibrium. Forces at thermal equilibrium are readily obtained as a particular case. As an illustration of this general theoretical framework, we show on three-body systems how the presence of a fourth slab can impact equilibrium temperatures in heat-transfer problems and equilibrium positions resulting from the forces acting on the system.
The 58‐kDa microspherule protein (MSP58), a nucleolar protein, interacts with nucleolar protein p120 (1998)

Protein p120 is a proliferation-related nucleolar protein which is detectable early in the G1 phase of the cell cycle and peaks early in the S phase. Most human malignant tumors contain much higher levels of protein p120 than normal resting cells. To identify p120-associated protein(s), a yeast two-hybrid screen was carried out using protein p120 as the bait. Two positive clones encoded portions of a novel protein, designated microspherule protein 58 kDa (MSP58). MSP58 mRNA is 1.9 kb and encodes an approximately 58-kDa polypeptide of 462 amino acids as shown by Western blotting of HeLa nucleolar proteins. The mouse MSP58 homolog has 97% amino acid similarity to human MSP58, but no MSP58 homolog was found in the yeast genome. The MSP58 N-terminal region contains serine-rich clusters and its C-terminal region has a coiled-coil domain. In insect Sf9 cells, recombinant p120 and MSP58 proteins associated with each other, confirming the results of the yeast two-hybrid assay. Deletion mutations revealed that the binding of MSP58 to p120 required a previously unrecognized coiled-coil domain within the N-terminal region of p120 and the C-terminal region of MSP58 protein. Immunofluorescence indicated that the MSP58 protein is localized in microspherules in the nucleolus. Anti-MSP58 Ig labeled nucleolar 'caps' when HeLa cells were treated with actinomycin D. When the MSP58 protein was overexpressed in COS-7 cells, the nucleolus became irregularly enlarged, which suggests that MSP58 may affect the size and shape of the nucleolus.
Supplementary Figure 4 from A Role for Homologous Recombination and Abnormal Cell-Cycle Progression in Radioresistance of Glioma-Initiating Cells (2023)

&lt;p&gt;PDF file, 159K, Long-term growth of neurosphere cultures following IR treatment.&lt;/p&gt;
Sequence data handling by computer (1977)

The speed of the new DNA sequencing techniques has created a need for computer programs to handle the data produced. This paper describes simple programs designed specifically for use by people with little or no computer experience. The programs are for use on small computers and provide facilities for storage, editing and analysis of both DNA and amino acid sequences. A magnetic tape containing these programs is available on request.
Stable SRAM cell design for the 32 nm node and beyond (2005)

SRAM cell stability will be a primary concern for future technologies due to variability and decreasing power supply voltages. 6T-SRAM can be optimized for stability by choosing the cell layout, device threshold voltages, and the /spl beta/ ratio. 8T-SRAM, however, provides a much greater enhancement in stability by eliminating cell disturbs during a read access, thus facilitating continued technology scaling. We demonstrate the smallest 6T (0.124/spl mu/m/sup 2/ half-cell) and full 8T (0.1998/spl mu/m/sup 2/) cells to date.
Video delivery over cellular wireless networks using EBR techniques (2005)

We propose a scheme for efficient transport of video over wireless networks using a novel rate control scheme. The explicit bit rate (EBR) control specifies the use of a variable rate channel and provides an adaptively varying requisite bandwidth to carry varying video encoded output. Due to the use of prediction and variable length codes (VLC) for video codecs, variable-bit-rate (VBR) encoding is considered logical in all advanced video encoders, such as H.263 and H.264. The VBR method of rate control which is currently employed in 3G networks requires the use of a constant bit rate (CBR) physical channel to carry video transmissions to ensure a fixed bandwidth channel to the user during a video call. However, a constant bit rate channel can result in delivering video frames in unequal time intervals, delays in transmission and poor video quality at the end user. We show the application of an explicit bit rate (EBR) control mechanism for high efficiency and quality video transmission for both cdma2000 1x and WCDMA wireless networks.
Overnight Shift From Obstructive to Central Apneas in Patients With Heart Failure (2001)

In patients with CHF, the shift from OSA to CSA is associated with a reduction in PCO(2). This appears to be related to an overnight deterioration in cardiac function as suggested by the concurrent lengthening of circulation time. Therefore, in CHF patients, alterations in cardiac function may influence apnea type.
Evidence that Receptor Aggregation may Play a Role in Transmembrane Signaling through the Insulin-Like Growth Factor-I Receptor (1988)

alpha IR-3 is a mouse monoclonal antibody that binds to an epitope on the human insulin-like growth factor I (IGF-I) receptor and inhibits [125I]IGF-I binding to this receptor on human skin fibroblasts (HSF) and Hep G2 human hepatoblastoma cells. Unlike the natural ligand (IGF-I), neither intact alpha IR-3 nor its monovalent Fab fragment stimulate aminoisobutyric acid (AIB) uptake in HSF, and both competitively antagonize IGF-I's ability to produce this effect. However, when HSF are incubated with alpha IR-3 or its Fab' fragment, subsequent exposure to anti-mouse immunoglobulin G (IgG) produces a potent stimulation of AIB uptake. Anti-Mouse IgG by itself does not effect AIB uptake. alpha IR-3 also antagonizes IGF-I's ability to stimulate glycogen synthesis in Hep G2 cells. As with AIB uptake in HSF, the combination of alpha IR-3 followed by anti-mouse IgG stimulates glycogen synthesis in Hep G2 cells to the same extent as that produced by IGF-I. The triggering of these two biological effects depends on the concentration of both alpha IR-3 and anti-mouse IgG. These results are consistent with the possibility that local aggregation or cross-linking of IGF-I receptors plays an important role in transmembrane signaling by this receptor.
Multi-chip module technology (2002)

Multi-Chip Modules (MCMs) are typically composed of complex devices mounted into single dense packages. Most MCMs today are used either in high performance systems, including mainframes and telecommunication equipment, or are placed in miniaturization driven applications, such as portable computers, consumer products, and personal communicators. Complex parallel processing products based on neural networks are natural candidates for the MCM technology. As is the case with any state-of-the-art solution adopters, MCM technology users must become familiar with multi-disciplinary aspects of this technology. This paper introduces today's MCM technology, and analyzes a number of these aspects, emphasizing on fundamentals of MCM manufacturing.
Leveraging Administrative Data for Bias Audits: Assessing Disparate Coverage with Mobility Data for COVID-19 Policy (2020)

Anonymized smartphone-based mobility data has been widely adopted in devising and evaluating COVID-19 response strategies such as the targeting of public health resources. Yet little attention has been paid to measurement validity and demographic bias, due in part to the lack of documentation about which users are represented as well as the challenge of obtaining ground truth data on unique visits and demographics. We illustrate how linking large-scale administrative data can enable auditing mobility data for bias in the absence of demographic information and ground truth labels. More precisely, we show that linking voter roll data -- containing individual-level voter turnout for specific voting locations along with race and age -- can facilitate the construction of rigorous bias and reliability tests. These tests illuminate a sampling bias that is particularly noteworthy in the pandemic context: older and non-white voters are less likely to be captured by mobility data. We show that allocating public health resources based on such mobility data could disproportionately harm high-risk elderly and minority groups.
Metabolic Capability and Phylogenetic Diversity of Mono Lake during a Bloom of the Eukaryotic Phototroph Picocystis sp. Strain ML (2018)

Algal blooms in lakes are often associated with anthropogenic eutrophication; however, they can occur without the human introduction of nutrients to a lake. A rare bloom of the alga <i>Picocystis</i> sp. strain ML occurred in the spring of 2016 at Mono Lake, a hyperalkaline lake in California, which was also at the apex of a multiyear-long drought. These conditions presented a unique sampling opportunity to investigate microbiological dynamics and potential metabolic function during an intense natural algal bloom. We conducted a comprehensive molecular analysis along a depth transect near the center of the lake from the surface to a depth of 25 m in June 2016. Across sampled depths, rRNA gene sequencing revealed that <i>Picocystis</i>-associated chloroplasts were found at 40 to 50% relative abundance, greater than values recorded previously. Despite high relative abundances of the photosynthetic oxygenic algal genus <i>Picocystis</i>, oxygen declined below detectable limits below a depth of 15 m, corresponding with an increase in microorganisms known to be anaerobic. In contrast to previously sampled years, both metagenomic and metatranscriptomic data suggested a depletion of anaerobic sulfate-reducing microorganisms throughout the lake's water column. Transcripts associated with photosystem I and II were expressed at both 2 m and 25 m, suggesting that limited oxygen production could occur at extremely low light levels at depth within the lake. Blooms of <i>Picocystis</i> appear to correspond with a loss of microbial activity such as sulfate reduction within Mono Lake, yet microorganisms may survive within the sediment to repopulate the lake water column as the bloom subsides.<b>IMPORTANCE</b> Mono Lake, California, provides a habitat to a unique ecological community that is heavily stressed due to recent human water diversions and a period of extended drought. To date, no baseline information exists from Mono Lake to understand how the microbial community responds to human-influenced drought or algal bloom or what metabolisms are lost in the water column as a consequence of such environmental pressures. While previously identified anaerobic members of the microbial community disappear from the water column during drought and bloom, sediment samples suggest that these microorganisms survive at the lake bottom or in the subsurface. Thus, the sediments may represent a type of seed bank that could restore the microbial community as a bloom subsides. Our work sheds light on the potential photosynthetic activity of the halotolerant alga <i>Picocystis</i> sp. strain ML and how the function and activity of the remainder of the microbial community responds during a bloom at Mono Lake.