gebhart/patrepeval huggingface dataset:
Lifelong Learning of Discriminative Representations. (2014)

We envision a machine learning service provider facing a continuous stream of problems with the same input domain, but with output domains that may differ. Clients present the provider with problems implicitly, by labeling a few example inputs, and then ask the provider to train models which rea-sonably extend their labelings to novel inputs. The provider wants to avoid constraining its users to a set of common la-bels, so it does not assume any particular correspondence be-tween labels for a new task and labels for previously encoun-tered tasks. To perform well in this setting, the provider needs a representation of the input domain which, in expectation, permits effective models for new problems to be learned effi-ciently from a small number of examples. While this bears a resemblance to settings considered in previous work on mul-titask and lifelong learning, our non-assumption of inter-task label correspondence leads to a novel algorithm: Lifelong Learner of Discriminative Representations (LLDR), which explicitly minimizes a proxy for the intra-task small-sample generalization error. We examine the relative benefits of our approach on a diverse set of real-world datasets in three sig-nificant scenarios: representation learning, multitask learning and lifelong learning. 1
Synthesis of Palladium Nanoparticles by Electrode-Respiring Geobacter sulfurreducens Biofilms (2023)

The electroactive microorganism Geobacter sulfurreducens can couple organic electron donor oxidation to the respiration of electrode surfaces, colonizing them in the process. These microbes can also reduce soluble metal ions, such as soluble Pd, resulting in metallic nanoparticle (NP) synthesis. Such NPs are valuable catalysts for industrially relevant chemical production; however, their chemical and solid-state synthesis are often energy intensive and result in hazardous biproducts. Utilizing electroactive microbes for precious metal NP synthesis has the advantage of operating under more sustainable conditions. By combining G. sulfurreducens’ ability to colonize electrodes and synthesize NPs, we performed electrode cultivation ahead of biogenic Pd(0) NP synthesis for the self-assembled fabrication of a biohybrid cell-Pd material. G. sulfurreducens biofilms were grown in electrochemical reactors with added Pd(II), and electrochemistry, spectroscopy, and electron microscopy were used to confirm (1) metabolic current production before and after Pd(II) addition, (2) simultaneous electrode respiration and soluble Pd reduction over time, and (3) biofilm-localized Pd NP synthesis. Utilizing electroactive microbes for the controlled synthesis of NPs can enable the self-assembly of novel cell-nanoparticle biohybrid materials with unique electron transport and catalytic properties.
Effect of a special screened greenhouse covered by fine mesh on maize outcrossing (2006)

Risk assessment and management of gene flow via pollen dispersal from genetically modified (GM) plants is critical. To minimize the likelihood of undesirable outcrossing, it is important to better understand the relationship between pollen dispersal distance and outcrossing rate in objective materials under physical containment. This study examined how a special screened greenhouse for Type-2 use, covered by a fine, 1-mm mesh reduced pollen dispersal and affected the outcrossing rate of non-GM yellow maize in the greenhouse and silver maize outside the greenhouse. Results suggest that the mesh-covered greenhouse was effective in reducing the outcrossing rate as a whole, although it may be less effective in reducing the longest distance of pollen dispersal. Further, the isolation distance threshold for the screened greenhouse is discussed in relation to risk assessment.
Cryptic Pockets Repository through Pocket Dynamics Tracking and Metadynamics on Essential Dynamics Space: Applications to Mcl-1 (2021)

Detection of cryptic pockets (hidden protein pockets) is a hot topic in structure-based drug discovery, especially for drugging the yet undruggable proteome. The experimental detection of cryptic pockets is still considered an expensive endeavor. Thus, computational methods, such as atomistic simulations, are used instead. These simulation methods can provide a perspective on protein dynamics that overpasses the experimental X-ray structures' static and average view. Nonetheless, unbiased molecular dynamics (MD) simulations fall short to detect transient and cryptic pockets requiring the crossing of high-energy barriers. Enhanced sampling methods, such as Metadynamics, provide a solution to overcome the time-scale problem faced by unbiased MD simulations. However, these methods are still limited by the availability of collective variable space to capture the intricate parameters, leading to the opening of cryptic pockets. Unfortunately, the design of such collective variables requires a priori knowledge of the binding site, information that is by definition lacking for cryptic pockets. In this work, we evaluated the use of the Metadynamics biasing scheme on essential coordinates space as a general method for cryptic pocket detection. This approach was applied to an antiapoptotic protein: Mcl-1 as a test model. In addition to providing a broader characterization of Mcl-1's conformational space, we show the effectiveness of this method in drawing the full repository of Mcl-1's known and novel cryptic pockets in an unsupervised manner.
Feeding obese dogs during weight loss is on average cost‐neutral (2015)

Knowledge that average diet costs do not significantly differ from food costs prior to weight loss may help veterinarians to persuade owners to enrol obese dogs in a weight management programme.
The Effects of a Stationary Surface Pocket on EHL Line Contact Start-Up (2004)

In this paper, the start-up process of line contact elastohydrodynamic lubrication with a stationary central surface pocket is studied. The solution of the pressure profile and film thickness distribution in the contact area is achieved by using a mixed lubricated-solid contact model. The mass balance of pocket lubricant flow is enforced by using a simple algorithm which adjusts the pocket cavitation boundary. With the surface pocket in the center of contact, the Hertzian contact area is divided into two micro-EHL contacts: the inlet micro-EHL contact and the outlet micro-EHL contact. The amount of lubricant trapped inside the pocket determines the overall start-up behavior. If the lubricant trapped is less than a critical amount, the two micro-EHL contact would be in start-up condition in serial: the lubricant film builds up in the inlet micro-EHL contact area first and then the lubricant film builds up in the outlet micro-EHL contact after the inlet lubricant flow fills the pocket. The start-up time in this case is longer than the start-up time for smooth surface start-up. If the lubricant trapped is more than the critical amount, the two micro-EHL contact would be in start-up condition in parallel: a lubricant film builds up in the inlet micro-EHL contact and at the same time a lubricant film builds up in the outlet micro-EHL contact. The start-up time in this case is much smaller than that of the smooth surface start-up. Compared with the smooth surface start-up condition, because the solid contact vanishes faster, there would be less frictional heat generated in the contact area and thus the surface temperature rise during the start-up process would be much smaller. These effects could prove beneficial in applications with frequent start and stop or oscillating running conditions, in which direct solid to solid contact occurs at the start (restart) of motion.
Hydrogen production optimization from methanol partial oxidation via ultrasonic sprays using response surface methodology and analysis of variance (2022)

Summary Hydrogen production via partial oxidation of methanol (POM) in an ultrasonic spray system was studied experimentally, using an h‐BN‐Pt/Al 2 O 3 catalyst with ultra‐low Pt contents (0.2 wt%). The effects of oxygen‐to‐methanol (O 2 /C) ratio, methanol flow rate, and gas hourly space velocity (GHSV) of air and carrier gas on H 2 yield were examined. Compared to conventional spray systems, the ultrasonic spray system could produce more uniformly dispersed methanol and thus further enhance the POM reaction. The results showed a higher O 2 /C ratio (0.8) enhanced the POM, which poses higher CH 3 OH conversion, higher reaction temperature, and lower CO and CH 4 productions. The CO 2 concentration was mainly affected by GHSV and CH 3 OH flow rate. A higher GHSV led to a quicker retention time for the reactants in the catalyst bed, and a lower CH 3 OH flow rate deteriorates the CO 2 concentration. Based on the Box Behnken design (BBD) from response surface methodology (RSM) and analysis of variance (ANOVA), the optimal operating conditions are found to be O 2 /C ratio = 0.8, CH 3 OH flow rate = 0.7 mL min −1 , and GHSV = 10 000 h −1 . Combining these conditions, the predicted maximum H 2 yield is 1.635 mol‧(mol CH 3 OH) −1 which is close to the experimental value of 1.646 mol‧(mol CH 3 OH) −1 . The RSM and ANOVA not only resulted in a quadratic response surface regression model and significant regression coefficients but also indicated CH 3 OH flow rate being the primary factor.
Ulnocarpal-Spanning Plate Fixation as a Novel Technique for Complex Distal Ulna Fracture (2020)

This case describes the original use of a wrist spanning plate for a complex distal ulna fracture. Ulnocarpal-spanning plate fixation provides an alternative to traditional methods of fixation.
Abstract B230: Targeting mitochondria for metastatic lung adenocarcinoma specific lethality. (2013)

Abstract Introduction: Lung cancer is the leading cause of cancer deaths in the United States. Its ability to leave the primary tumor and establish inoperable metastasis impairs successful therapy and is a major contributor to its lethality. A genetically engineered mouse model recapitulates the human disease very well, incorporating conditional alleles of the Kras oncogene and p53 tumor suppressor. Recently, cell lines generated from non-metastatic primary lung tumors (TnonMet) and metastases (Met) in this model were shown to maintain their metastatic state and exhibit dramatic differences in gene expression programs. This unique set of cell lines from early stage non-metastatic tumors and late-stage metastases provides an opportunity to understand whether cancer progression also creates unique vulnerabilities. Experimental design: A pooled lentiviral-shRNA library screen which targeted ∼20,000 genes with &amp;gt;92,000 shRNA in two TnonMet and two Met cell lines was used to systematically uncover genes that are specifically required to sustain metastasis survival or growth. High-throughput sequencing of the shRNA in the cancer cell populations before and after 20 population doublings in culture identified shRNAs that disadvantaged each cell line. Gene-set enrichment algorithm was utilized to analyse the data. qRT-PCR, cell competition assays and mitochondria-specific dyes were used to verify the results and unravel the underlying mechanism. Results and Conclusion: The analysis of our pooled shRNA screen revealed mitochondrial ribosomal protein (Mrp) complexes as the top two gene-sets; in fact individual shRNA targeting more than 15 Mrp genes selectively disadvantaging Met cells with minimal impact on TnonMet cells. These results were individually verified with qRT-PCR. Interestingly, Met cells showed increased expression of mitochondria encoded genes, pointing to a strong imbalance in mitochondrial homeostasis. Furthermore, mitochondria-targeted therapy blocking mitochondrial translation or replication significantly inhibited Met cell growth more than TnonMet cell growth. Taken together, these results point to mitochondria as a metastasis-specific therapeutic target in lung adenocarcinoma and need to be further investigated. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B230. Citation Format: Barbara M. Gruener, Chen-Hua Chuang, Ian Linde, Shin-Heng Chiou, Ben Readhead, Joel Dudley, John Doench, David Root, Monte M. Winslow. Targeting mitochondria for metastatic lung adenocarcinoma specific lethality. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B230.
Epi-LASIK: Comparative histological evaluation of mechanical and alcohol-assisted epithelial separation (2003)

To compare the effect of mechanical and alcohol-assisted excision on the histological ultrastructure of epithelial disks from human corneas. Vardinoyiannion Eye Institute of Crete, University of Crete, Medical School, Crete, Greece. Ten eyes of 10 patients were deepithelialized by 1 of 2 two techniques. In 6 eyes, a customized instrument was used to mechanically separate the epithelial layer. In 4 eyes, the epithelial disks were obtained using the conventional laser-assisted subepithelial keratectomy (LASEK) technique; that is, with alcohol concentrations of 15% and 20%. All specimens were assessed by light and electron microscopy, and the histological findings of the 2 methods were compared. Transmission electron microscopy showed that when the epithelial disks were excised by mechanical separation, the lamina densa and lamina lucida were preserved and the hemidesmosomes had normal morphology along almost the entire length of the basement membrane. The basal epithelial cells of the separated epithelial disks showed minimal trauma and edema. Specimens obtained using 15% and 20% alcohol concentrations showed formation of cytoplasmic fragments of the basal epithelial cells, enlargement of the intercellular spaces, and extensive discontinuities in the basement membrane, which was excised at the level of the lamina lucida. Mechanical separation did not affect the normal cell morphology of the excised epithelial disks. Transmission electron microscopy of the specimens proved the manual technique is less invasive to epithelial integrity than LASEK using either alcohol concentration.
A 184nW, 121µg/√Hz Noise Floor Triaxial MEMS Accelerometer with Integrated CMOS Readout Circuit and Variation-Compensated High Voltage MEMS Biasing (2022)

We present a triaxial MEMS accelerometer readout circuit (RoC) with 40× signal gain using a high MEMS bias voltage, reducing power by eliminating the need for a chopped AFE chain. The proposed RoC achieves a 121µg/√Hz input referred noise and 1.5g dynamic range at 184nW per-axis power, while maintaining <1% non-linearity and a mechanical full-scale of >20 g, improving FoM by 15.6×.
Feature-Based Synthesis: A Tool For Evaluating, Designing, And Interacting With Music Ir Systems. (2006)

[TODO] Add abstract here.
Association of <i>DRD4</i> polymorphism with severity of oppositional defiant disorder, separation anxiety disorder and repetitive behaviors in children with autism spectrum disorder (2010)

The objective was to examine whether a common polymorphism in the dopamine D4 receptor gene (DRD4) might be a potential biomarker for behavioral variation within the autism spectrum disorder clinical phenotype. Children (N=66) were evaluated with a validated mother- and teacher-completed DSM-IV-referenced rating scale. Partial eta-squared (ηp(2) ) was used to gauge the magnitude of group differences: 0.01-0.06=small, 0.06-0.14=moderate and >0.14=large. Children who were 7-repeat allele carriers had more severe oppositional defiant disorder behaviors according to mothers' (ηp(2)=0.10) and teachers' (ηp(2)=0.06) ratings than noncarriers, but the latter was marginally significant (P=0.07). Children who were 7-repeat allele carriers also obtained more severe maternal ratings of tics (ηp(2)=0.07) and obsessions-compulsions (ηp(2)=0.08). Findings for maternal ratings of separation anxiety were marginally significant (P=0.08, ηp(2) =0.05). Analyses of combined DRD4 and dopamine transporter gene (DAT1) genotypes approached significance (P=0.05) for teachers' ratings of oppositional behavior and mothers' ratings of tics. DRD4 allelic variation may be a prognostic biomarker for challenging behaviors in children with autism spectrum disorder, but these exploratory findings remain tentative pending replication with larger independent samples.
a rel-Related Polypeptide (1991)

Garry P. Nolan,* Sankar Ghosh,’ Hsiou-Chi Liou,’ Paul Tempst,t and David Baltimore”* *Whitehead Institute for Biomedical Research Nine Cambridge Center Cambridge, Massachusetts 02142 tHoward Hughes Medical Institute and Department of Genetics Harvard Medical School Boston, Massachusetts 02215 SRockefeller University New York, New York 10021 Summary The sequence and biochemical properties of the prod- Nuct of the cloned cDNA for the ~65 subunit of nuclear ,factor
Decontamination of disposable respirators for reuse in a pandemic employing in-situ-generated peracetic acid (2021)

The simple application and widespread availability of 6%AA/6%HP solution for decontaminating disposable FFPs make this solution globally viable, including developing and third world countries.
Identification of plasma protein biomarkers associated with idiopathic pulmonary arterial hypertension (2006)

We have employed SELDI-TOF MS to screen for differentially expressed proteins in plasma samples from 27 patients with idiopathic pulmonary arterial hypertension (IPAH) and 26 healthy controls. One ion (m/z approximately 8600) that was found to be elevated in IPAH was validated by SELDI-TOF MS analysis of a second and separate set of plasma samples comprising 30 IPAH patients and 19 controls. The m/z 8600 was purified from plasma by sequential ion exchange and reverse-phase chromatographies and SDS-PAGE. It was identified, following trypsin digestion, by MS peptide analysis as the complement component, complement 4a (C4a) des Arg. Plasma levels of C4a des Arg measured by ELISA confirmed that the levels were significantly higher (p < 0.0001) in IPAH patients (2.12 +/- 0.27 microg/mL) compared with normal controls (0.53 +/- 0.05 microg/mL). A cut-off level of 0.6 microg/mL correctly classified 92% of IPAH patients and 80% of controls. Further studies will be needed to determine its performance as a diagnostic biomarker, whether used alone or in combination with other biomarkers. Nevertheless, this study demonstrates that putative biomarkers characteristic of IPAH can be identified using a conjoint SELDI-TOF MS - proteomics approach.
Catalytic Activity of Partially Oxidized Tantalum Carbonitride for Oxygen Reduction Reaction (2009)

A partially oxidized TaC0.58N0.42 (Ta-CNO) has been investigated as a new cathode for polymer electrolyte fuel cells. TaC0.58N0.42 and completely oxidized Ta2O5 had poor catalytic activity for oxygen reduction reaction (ORR). On the other hand, the Ta-CNO had a high catalytic activity for the ORR. The onset potential on the Ta-CNO for the ORR had a maximum value of 0.91 V vs. RHE in 0.1 mol dm-3 H2SO4 at 30oC. This result indicates that the partial oxidation of TaC0.58N0.42 was essential to enhance the catalytic activity for the ORR. A mixing of the Ta-CNO with Ketjen Black was required to increase both the oxygen reduction current and the onset potential of the ORR. The single cell test was performed using Ta-CNO as a cathode under pressurized condition. The open circuit voltage was 0.91 V, and the maximum power density reached 220 mW cm-2.
&lt;title&gt;Optical sensor for detecting missile fuel leaks&lt;/title&gt; (2000)

Missiles represent strategic weapons in modern warfare. They are stored prior to deployment, and they need to be kept in flight-ready condition during storage. It is therefore necessary to promptly detect any missile fuel leakage. Intelligent Optical Systems initiated an effort to develop a breakthrough device that combines a long period grating- based chemical sensor with neural network software. These reversible sensors perform real-time measurements of liquid fuel components.
Learning data-driven reduced elastic and inelastic models of spot-welded patches (2021)

Solving mechanical problems in large structures with rich localized behaviors remains a challenging issue despite the enormous advances in numerical procedures and computational performance. In particular, these localized behaviors need for extremely fine descriptions, and this has an associated impact in the number of degrees of freedom from one side, and the decrease of the time step employed in usual explicit time integrations, whose stability scales with the size of the smallest element involved in the mesh. In the present work we propose a data-driven technique for learning the rich behavior of a local patch and integrate it into a standard coarser description at the structure level. Thus, localized behaviors impact the global structural response without needing an explicit description of that fine scale behaviors.
Cloning and characterization of a novel Drosophila Wnt gene, Dwnt-5, a putative downstream target of the homeobox gene Distal-less (1992)

The Wnt gene family in vertebrates comprises at least 11 distinct genes but the only family member previously identified in Drosophila has been the segment polarity gene wingless (wg), the ortholog of vertebrate Wnt-1. In this report we describe the isolation of a novel Drosophila Wnt gene, Dwnt-5, which differs significantly from wg in both the pattern of its expression during embryogenesis and the predicted structure of its product. Dwnt-5 encodes a polypeptide of 112 kDa, which is more than twice as large as the products of previously known Wnt genes. The protein shares homology with other Wnt sequences in its carboxy-terminal half only and is most closely related to the products of vertebrate Wnt-5a and Wnt-5b. Dwnt-5 is expressed in a complex pattern during Drosophila embryogenesis. At the extended germ band stage, however, transcripts accumulate specifically in the nascent limb primordia of the head and thoracic segments. We show that this elevated expression depends on the activity of the homeobox gene Distal-less (Dll) and suggest that the Dwnt-5 gene may constitute a downstream target of Dll that acts in the specification of these primordia.
Synchronization: Why and How to Avoid It (2019)

Let us underscore this up front: if you don’t need to use the synchronization features described in this chapter, so much the better. Here, we cover synchronization mechanisms and alternatives to achieve mutual exclusion. “Synchronization” and “exclusion” should have quite a negative connotation for parallel programmers caring about performance. These are operations that we want to avoid because they cost time and, in some cases, processor resources and energy. If we can rethink our data structures and algorithm so that it does not require synchronization nor mutual exclusion, this is great! Unfortunately, in many cases, it is impossible to avoid synchronization operations, and if this is your case today, keep reading! An additional take-home message that we get from this chapter is that careful rethinking of our algorithm can usually result in a cleaner implementation that does not abuse synchronization. We illustrate this process of rethinking an algorithm by parallelizing a simple code following first a naïve approach that resorts to mutexes, evolve it to exploit atomic operations, and then further reduce the synchronization between threads thanks to privatization and reduction techniques. To this final end, we show how to leverage thread local storage (TLS) as a way to avoid highly contended mutual exclusion overhead. In the sequel, we assume you are, to some extent, familiarized with the concepts of “lock,” “shared mutable state,” “mutual exclusion,” “thread safety,” “data race,” and other synchronization-related issues. If not, a gentle introduction to them is provided in the Preface of this book.