gebhart/patrepeval huggingface dataset:
The Power of External Memory in Increasing Predictive Model Capacity (2023)

One way of introducing sparsity into deep networks is by attaching an external table of parameters that is sparsely looked up at different layers of the network. By storing the bulk of the parameters in the external table, one can increase the capacity of the model without necessarily increasing the inference time. Two crucial questions in this setting are then: what is the lookup function for accessing the table and how are the contents of the table consumed? Prominent methods for accessing the table include 1) using words/wordpieces token-ids as table indices, 2) LSH hashing the token vector in each layer into a table of buckets, and 3) learnable softmax style routing to a table entry. The ways to consume the contents include adding/concatenating to input representation, and using the contents as expert networks that specialize to different inputs. In this work, we conduct rigorous experimental evaluations of existing ideas and their combinations. We also introduce a new method, alternating updates, that enables access to an increased token dimension without increasing the computation time, and demonstrate its effectiveness in language modeling.
The Partial Support of the Left Ventricular Assist Device Shifts the Systemic Cardiac Output Curve Upward in Proportion to the Effective Left Ventricular Ejection Fraction in Pressure-Volume Loop (2020)

Left ventricular assist device (LVAD) has been saving many lives in patients with severe left ventricular (LV) failure. Recently, a minimally invasive transvascular LVAD such as Impella enables us to support unstable hemodynamics in severely ill patients. Although LVAD support increases total LV cardiac output (CO<sub>TLV</sub>) at the expense of decreases in the native LV cardiac output (CO<sub>NLV</sub>), the underlying mechanism determining CO<sub>TLV</sub> remains unestablished. This study aims to clarify the mechanism and develop a framework to predict CO<sub>TLV</sub> under known LVAD flow (CO<sub>LVAD</sub>). We previously developed a generalized framework of circulatory equilibrium that consists of the integrated CO curve and the VR surface as common functions of right atrial pressure (P<sub>RA</sub>) and left atrial pressure (P<sub>LA</sub>). The intersection between the integrated CO curve and the VR surface defines circulatory equilibrium. Incorporating LVAD into this framework indicated that LVAD increases afterload, which in turn decreases CO<sub>NLV</sub>. The total LV cardiac output (CO<sub>TLV</sub>) under LVAD support becomes CO<sub>TLV</sub> = CO<sub>NLV</sub>+EF<sub>e</sub> · CO<sub>LVAD</sub>, where EF<sub>e</sub> is effective ejection fraction, i.e., E<sub>es</sub>/(E<sub>es</sub>+E<sub>a</sub>). E<sub>es</sub> and E<sub>a</sub> represent LV end-systolic elastance (E<sub>es</sub>) and effective arterial elastance (E<sub>a</sub>), respectively. In other words, LVAD shifts the total LV cardiac output curve upward by EF<sub>e</sub> · CO<sub>LVAD</sub>. In contrast, LVAD does not change the VR surface or the right ventricular CO curve. In six anesthetized dogs, we created LV failure by the coronary ligation of the left anterior descending artery and inserted LVAD by withdrawing blood from LV and pumping out to the femoral artery. We determined the parameters of the CO curve with a volume-change technique. We then changed the CO<sub>LVAD</sub> stepwise from 0 to 70-100 ml/kg/min and predicted hemodynamics by using the proposed circulatory equilibrium. Predicted CO<sub>TLV</sub>, P<sub>RA</sub>, and P<sub>LA</sub> for each step correlated well with those measured (SEE; 2.8 ml/kg/min 0.17 mmHg, and 0.65 mmHg, respectively, r<sup>2</sup>; 0.993, 0.993, and 0.965, respectively). The proposed framework quantitatively predicted the upward-shift of the total CO curve resulting from the synergistic effect of LV systolic function and LVAD support. The proposed framework can contribute to the safe management of patients with LVAD.
Supplementary Figure S2 from Selective Modulation of a Pan-Essential Protein as a Therapeutic Strategy in Cancer (2023)

&lt;p&gt;NXT1 is a selective and lethal dependency in neuroblastoma&lt;/p&gt;
Gender and disease severity determine proximal femoral morphology in developmental dysplasia of the hip (2019)

In this computed tomography (CT) morphological study we describe the way the proximal femoral morphology differs with worsening degrees of developmental dysplasia of the hip (DDH) and describe gender differences in patients with DDH. Forty-nine male patients with DDH were matched with 49 females with DDH, using age and the Crowe classification of DDH severity. The femoral length, anteversion, neck-shaft angle, offset, neck length, canal-calcar ratio, canal flare index, lateral center-edge angle, alpha angle, pelvic tilt, and pelvic incidence were measured for each patient on their pre-operative CT scans, prior to total hip arthroplasty surgery. Femoral anteversion and neck length were 16° and 47 mm, 25°and 36 mm, 26° and 43 mm, and 44° and 36 mm, for Crowe I and III males and Crowe I and III females, respectively. The mean male anteversion was 22° (±14), compared to 30° (±15.5) in females (p = 0.02, Confidence Interval: 1.6-14.9). Gender differences in femoral length, neck length and offset lost significance when height-normalized and no other significant gender differences were found. In conclusion, femoral neck length reduces with increasing DDH severity, whilst anteversion tends to increase. Male patients with DDH have significantly less femoral anteversion, which has important implications for osteotomy and arthroplasty surgery in DDH. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.
PV Hourly Simulation Tool (2010)

This software requires inputs of simple general building characteristics and usage information to calculate the energy and cost benefits of solar PV. This tool conducts and complex hourly simulation of solar PV based primarily on the area available on the rooftop. It uses a simplified efficiency calculation method and real panel characteristics. It includes a detailed rate structure to account for time-of-use rates, on-peak and off-peak pricing, and multiple rate seasons. This tool includes the option for advanced system design inputs if they are known. This tool calculates energy savings, demand reduction, cost savings, incentives and building life cycle costs including: simple payback, discounted payback, net-present value, and savings to investment ratio. In addition this tool also displays the environmental benefits of a project.
The Wheel‐Shaped Cu20 Tungstophosphate [Cu20Cl(OH)24(H2O)12 (P8W48O184)]25‐ Ion. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Modular POP Ligands in Rhodium‐Mediated Asymmetric Hydrogenation: A Comparative Catalysis Study (2012)

Abstract Highly efficient and enantioselective hydrogenation reactions for α‐(acylamino)acrylates, itaconic acid derivatives and analogues, α‐substituted enol ester derivatives, and α‐arylenamides (25 substrates) catalyzed by chiral cationic rhodium complexes of a set of POP ligands have been developed. The catalytic systems derived from these POP ligands provided a straightforward access to enantiomerically enriched α‐amino acid, carboxylic acid, amine, and alcohol derivatives that are valuable chiral building blocks. Excellent efficiencies (full conversion in all cases) and extremely high enantiomeric excesses (94–99% ee ) were achieved for a wide range of α‐substituted enol ester derivatives, regardless of the substitution pattern. The R‐oxy group of the ligand (methoxy or triphenylmethoxy) strongly influences the enantioselectivity and catalytic activity. Greater steric bulk around the metal centre correlated to greater (or similar) enantioselectivity, but also to slower hydrogenation. Furthermore, the hydrogenation rates observed with the four model substrates follow the same trend, independently of the R‐oxy group of the ligand: methyl 2‐acetamidoacrylate&gt;dimethyl itaconate&gt;1‐phenylvinyl acetate&gt; N ‐(1‐phenylvinyl)acetamide. A substrate‐to‐catalyst ratio (S/C) of up to 10,000:1 was sufficient for total hydrogenation of a model substrate of intermediate reactivity (dimethyl itaconate), and did not imply any loss in conversion or enantioselectivity.
Combinatorial group theory and public key cryptography (2004)

After some excitement generated by recently suggested public key exchange protocols due to Anshel-Anshel-Goldfeld and Ko-Lee et al., it is a prevalent opinion now that the conjugacy search problem is unlikely to provide sufficient level of security if a braid group is used as the platform. In this paper we address the following questions: (1) whether choosing a different group, or a class of groups, can remedy the situation; (2) whether some other "hard" problem from combinatorial group theory can be used, instead of the conjugacy search problem, in a public key exchange protocol. Another question that we address here, although somewhat vague, is likely to become a focus of the future research in public key cryptography based on symbolic computation: (3) whether one can efficiently disguise an element of a given group (or a semigroup) by using defining relations.
Supplementary Figure S1 from Tumor Cell–Autonomous SHP2 Contributes to Immune Suppression in Metastatic Breast Cancer (2023)

&lt;p&gt;Combination of SHP099 and α-PD-L1 delays D2.A1 pulmonary growth in vivo&lt;/p&gt;
LY2606368 Causes Replication Catastrophe and Antitumor Effects through CHK1-Dependent Mechanisms (2015)

CHK1 is a multifunctional protein kinase integral to both the cellular response to DNA damage and control of the number of active replication forks. CHK1 inhibitors are currently under investigation as chemopotentiating agents due to CHK1's role in establishing DNA damage checkpoints in the cell cycle. Here, we describe the characterization of a novel CHK1 inhibitor, LY2606368, which as a single agent causes double-stranded DNA breakage while simultaneously removing the protection of the DNA damage checkpoints. The action of LY2606368 is dependent upon inhibition of CHK1 and the corresponding increase in CDC25A activation of CDK2, which increases the number of replication forks while reducing their stability. Treatment of cells with LY2606368 results in the rapid appearance of TUNEL and pH2AX-positive double-stranded DNA breaks in the S-phase cell population. Loss of the CHK1-dependent DNA damage checkpoints permits cells with damaged DNA to proceed into early mitosis and die. The majority of treated mitotic nuclei consist of extensively fragmented chromosomes. Inhibition of apoptosis by the caspase inhibitor Z-VAD-FMK had no effect on chromosome fragmentation, indicating that LY2606368 causes replication catastrophe. Changes in the ratio of RPA2 to phosphorylated H2AX following LY2606368 treatment further support replication catastrophe as the mechanism of DNA damage. LY2606368 shows similar activity in xenograft tumor models, which results in significant tumor growth inhibition. LY2606368 is a potent representative of a novel class of drugs for the treatment of cancer that acts through replication catastrophe.
Improved survival of patients with hypermutation in uterine serous carcinoma (2015)

•Uterine serous carcinoma (USC) is an aggressive subtype of endometrial cancer.•Mutations in DNA polymerase ε gene (POLE) are detected in a subset of USC and confer a strong mutator phenotype.•USC patients diagnosed with POLE mutations experience a significantly better prognosis.
Joint Beamforming Design for Multiuser MISO Downlink Aided by a Reconfigurable Intelligent Surface and a Relay (2022)

Reconfigurable intelligent surfaces (RISs) have drawn considerable attention due to their ability to direct electromagnetic waves into desirable directions. Although RISs share some similarities with relays, the two have fundamental differences impacting their performance. To harness the benefits of both, we propose a downlink system wherein a relay and an RIS improve performance in terms of energy-efficiency. Using singular value decomposition (SVD), semidefinite programming (SDP), and function approximations, we propose different solutions for optimizing the beamforming matrices at the base-station (BS), the relay, and the phase shifts at the RIS to minimize the total power under quality-of-service (QoS) constraints. The problem is solved when the relay operates in half-duplex and full-duplex modes and when the reflecting elements have continuous and discrete phase shifts. Simulation results compare the performance of the system with and without the RIS or the relay, under different optimization solutions. The results show that the system with full-duplex relay and RIS outperforms the other scenarios, and the contribution of full-duplex relay is higher than that of the RIS. However, an RIS outperforms a half-duplex relay when the required QoS is high. The results also show that increasing the number of reflecting elements improves the performance better in the presence of a relay than in its absence.
IMMU-33. MULTI-ANTIGEN RECOGNITION CIRCUITS OVERCOME CHALLENGES OF SPECIFICITY, HETEROGENEITY, AND DURABILITY IN T-CELL THERAPY FOR GLIOBLASTOMA (2020)

Abstract Treatment of solid cancers with chimeric antigen receptor (CAR) T-cells is challenging because of a lack of target antigens that are both tumor-specific and homogenously expressed. While epidermal growth factor receptor (EGFR)vIII represents a glioblastoma (GBM)-specific antigen, its expression is heterogeneous within the tumor resulting in tumor escape. In contrast, more homogenously expressed GBM-associated antigens (GAA), such as EphA2, are non-ideal because of expression in other normal organs, yielding potential cross-reactive toxicity. As a way to safely target GAAs in the tumor without attacking normal cells expressing the same GAAs outside of the brain, we adapted a novel synthetic Notch (synNotch) receptor system and established a “prime and kill” sequential two-receptor CAR circuit. A synNotch receptor recognizes a specific priming antigen; the heterogeneous GBM neoantigen EGFRvIII or a brain tissue-specific antigen to prime the local expression of a CAR that mediates cytotoxicity against a GAA (e.g. EphA2). In orthotopic GBM6 glioma model, a patient-derived xenograft (PDX) with heterogeneous expression of EGFRvIII, intravenous infusion of T-cells transduced with EGFRvIII synNotch→anti-IL-13Rα2/EphA2 tandem CAR circuit resulted in long-term (over 100 days) survival and eradication of the heterogeneous tumor in all of 12 mice in two independent experiments. In contrast, constitutive CARs targeting EGFRvIII or IL-13Rα2/EphA2 (as a tandem CAR) failed to exhibit long-term anti-tumor response. Moreover, T-cells transduced with synNotch-regulated CAR maintain a less differentiated state which is associated with higher durability compared with ones with constitutive CAR in vivo. T-cells transduced with a synNotch→CAR circuit primed by a brain-specific antigen, myelin oligodendrocyte glycoprotein (MOG), exhibited a precise and potent local control of intracranial PDX without evidence of priming in extracranial organs. These data support the utility of synNotch→CAR circuits in EGFRvIII-negative GBM cases. By integrating multiple imperfect but complementary antigens, we improve both the specificity and persistence of T-cells directed against GBM.
An Enhanced Multi-path Scheme for QoS Guarantee in Wireless Sensor Network (2007)

A sensor network consists of a large number of sensor nodes that are densely deployed. The large scale sensor network is generally used for applications such as target tracking and emergency response rather than common data. The applications have real-time requirements that sensed data must be exactly delivered to a destination node within a given time. In this paper, we propose a multi-path scheme, which utilizes the virtual grid, to meet the real-time requirements. In order to select one of multi-paths depending on the service differentiation, the proposed scheme uses several information such as the size and transfer period of sensed data. In addition to an existing path, the proposed algorithm dynamically selects an alternative path according to multi-path environments. Moreover, it assigns the shortest path to the sensed data with most strict time restriction. Therefore, our scheme can guarantee the transmission reliability since sensed data is transmitted two or more routes by using the dualized multi-path on the virtual grid. In this paper, we introduce some realistic scenarios and propose an analytical model. Then performance of the proposed scheme is evaluated by numerical analysis. Our results show that the proposed scheme significantly outperforms the SPEED and MMSPEED.
Improving Information Retrieval with Textual Analysis: Bayesian Models and Beyond (2001)

Information retrieval (IR) is a difficult problem. While many have attempted to model text documents and improve search results by doing so, the most successful text retrieval to date has been developed in an ad-hoc manner. One possible reason for this is that in developing these models very little focus has been placed on the actual properties of text. In this thesis, we discuss a principled Bayesian approach we take to information retrieval, which we base on the standard IR probabilistic model. Not surprisingly, we find this approach to be less successful than traditional ad-hoc retrieval. Using data analysis to highlight the discrepancies between our model and the actual properties of text documents, we hope to arrive at a better model for our corpus, and thus a better information retrieval strategy. Specifically, we believe we will find it is inaccurate to assume that whether a term occurs in a document is independent of whether it has already occurred, and we will suggest a way to improve upon this without adding complexity to the solution.
Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili (2018)

Biosensors detect signals using biological sensing components such as redox enzymes and biological cells. Although cellular versatility can be beneficial for different applications, limited stability and efficiency in signal transduction at electrode surfaces represent a challenge. Recent studies have shown that the Mtr electron conduit from Shewanella oneidensis MR-1 can be produced in Escherichia coli to generate an exoelectrogenic model system with well-characterized genetic tools. However, means to specifically immobilize this organism at solid substrates as electroactive biofilms have not been tested previously. Here, we show that mannose-binding Fim pili can be produced in exoelectrogenic E. coli and can be used to selectively attach cells to a mannose-coated material. Importantly, cells expressing fim genes retained current production by the heterologous Mtr electron conduit. Our results demonstrate the versatility of the exoelectrogenic E. coli system and motivate future work that aims to produce patterned biofilms for bioelectronic devices that can respond to various biochemical signals.
Expression and Localization of Tenomodulin, a Transmembrane Type Chondromodulin-I-Related Angiogenesis Inhibitor, in Mouse Eyes (2003)

These results indicate a potential role for TeM in prevention of vascular invasion in the mouse eye and the possibility of both TeM and ChM-I as candidates for use in gene therapy approaches to treatment of ocular angiogenesis.
Effect of variation ofKlebsiella pneumoniae acetolactate synthase expression on metabolic flux redistribution inEscherichia coli (2000)

Escherichia coli strains carrying the Bacillus subtilis acetolactate synthase (ALS) gene were previously shown to produce less acetate with higher ATP yields. Metabolic flux analysis was used to show that excess pyruvate was channeled into the less inhibitory product, acetoin. To further understand the role of intrinsic enzymatic properties and the effect of variations in enzyme levels in the alternation of metabolic fluxes, we constructed a chromosomal integrant of the Klebsiella pneumoniae ALS gene. The reported in vitro Michaelis-Menten constants (K(m)) for the Bacillus and the Klebsiella ALS are 13.0 mM and 8.0 mM, respectively. Furthermore, expression of the Klebsiella ALS is under the control of an inducible trp promoter system. Shake-flask experiments showed a linear induction response (the ALS activity changes from about 9 to 223 U/mg of protein when the inducer concentration [IAA] varied from 0 to 40 mg/L). Chemostat experiments showed a similar induction response. Interactions between the branched reactions catalyzed by the PFL, LDH, and the ALS enzymes at the pyruvate node were examined. The results indicate the importance of in vivo enzyme activities in the redistribution of metabolic fluxes.
Higher ionic conductive ceria-based electrolytes for solid oxide fuel cells (2007)

Codoping is used to enhance the ionic conductivity of ceria-based electrolytes. Sm3+ and Nd3+ were selected as codopants to promote low migration energy paths for oxygen vacancy diffusion, thereby increasing the ionic conductivity. Moreover, the use of codopants also increases the pre-exponential factor in the Arrhenius relationship, thus further improving the ionic conductivity. The ionic conductivity of SmxNdxCe1−2xO2−δ solid solutions is measured using electrochemical impedance spectroscopy. It was observed that for Sm0.075Nd0.075Ce0.85O2−δ, the grain ionic conductivity was 14.0×10−3Scm−1 at 550°C, which makes it one of the most promising ceria-based electrolytes for intermediate temperature solid oxide fuel cells.
Hepatitis B, Transfusions and Renal Transplantation (1977)

Pirson and his colleagues report elsewhere in this issue of the Journal that patients found to have hepatitis B surface antigen (HBs Ag) in their circulation before or after renal transplantation have a fivefold increase in deaths (10 deaths in 61 patients) resulting from hepatic failure than HBs Ag-negative patients (two deaths in 60). This increased mortality, which was not noted in several previous series1 , 2 during shorter periods of observation, is first discerned three years after transplantation. At first glance, we found this report surprising since only 10 of 650 patients receiving transplants at our institution have died . . .
Effects of polarization rotation in optical ring-resonator-based devices (2006)

In this paper, polarization rotation due to optical waveguide bending is analytically and numerically investigated. It is shown that the process of polarization conversion in the bend strictly depends on the characteristics of the straight waveguide. The strength of polarization coupling linearly increases with the waveguide refractive index contrast, whereas birefringence is responsible for the phase mismatch that limits the conversion efficiency. Waveguides with refractive index profile symmetrical in the direction orthogonal to the plane of the bend do not exhibit polarization rotation. Inside optical ring resonators, polarization rotation induced by waveguide bending is found to be highly enhanced by the cavity effect, which gives rise to strongly frequency dependent polarization rotation and dramatically alters the ring's spectral response. In the case of single-ring phase shifters, polarization rotation is effectively described by means of an approach based on the theory of poles-zeros loci, which straightforwardly provides conditions for complete polarization conversion, also in the presence of birefringence and losses. The detrimental effects caused by undesired polarization coupling on the spectral response of widespread optical devices based on ring resonators are also discussed. From this point of view, birefringence is demonstrated to be beneficial to make optical components less sensitive to the effects of polarization rotation.