gebhart/patrepeval huggingface dataset:
Investigation on Fouling Mechanisms for Recombinant Human Growth Hormone Sterile Filtration (1998)

During sterile filtration of recombinant human growth hormone solutions, severe membrane fouling was experienced compared to other protein preparations of significantly higher molecular weights and concentrations. This phenomenon was attributed to rhGH aggregation/adsorption occurring in the filter pore. To better understand this phenomenon, we examined several possible fouling mechanisms: (1) pore constriction, (2) adsorption due to nonspecific binding between protein and the membrane, (3) shear-induced adsorption, (4) hydrophobic interface-induced aggregation/adsorption. The protein solutions were sterily filtered using 0.22 mm filters, and their filtration fluxes were monitored. Filtration on the capillary and the noncapillary filters suggested that constraints by pore constriction and tortuosity played only a limited role. Filtration using filters with different degrees of protein binding tendency suggested that nonspecific adsorption was insignificant. The shear stress acting on the protein during filtration was small. RhGH which was intentionally sheared in a high-speed concentrically rotating device did not aggravate fouling tendency, suggesting that the shear-induced adsorption might not be the major fouling mechanism. The dynamic light scattering data showed a trace amount of rhGH aggregates always present in equilibrium with the hydrophobic (air-water and membrane-water) interface. These aggregates tended to be adsorbed to the membrane, and more aggregates were generated presumably due to the equilibrium between aggregates and protein monomers. This adsorption/aggregation process eventually fouled the membrane. When the hydrophobic interface was occupied by surfactant molecules, the equilibration kinetics ceased to generate aggregates, thereby minimizing membrane fouling. This study clarified the cause of such an unusual fouling phenomenon upon microfiltration.
Group II Chaperonin in a Thermophilic Methanogen,Methanococcus thermolithotrophicus (1998)

A gene encoding 544 amino acids for a subunit of group II chaperonin (thermosome) was cloned from a thermophilic methanogen, Methanococcus thermolithotrophicus. The deduced amino acid sequence showed 66.5, 56.1, and 20.1% similarities to those of Methanopyrus kandleri and Thermoplasma acidophilum and group I chaperonin of Escherichia coli, respectively. We call this chaperonin MTTS (M. thermolithotrophicus thermosome). The MTTS gene was expressed in E. coli. The purified recombinant MTTS seemed to be monomeric on gel filtration in the absence of Mg2+ and ATP. The monomer assembled to an oligomer (complex) in the presence of 50 mM MgCl2, 0.25 mM ATP, and 0.3 M (NH4)2SO4. It was eluted immediately before the elution volume of E. coli GroEL tetradecamer on gel filtration with a TSKgel G3000SWXL column. This reconstructed MTTS complex showed the cylindrical structure with two stacked rings in electron microscopy. The MTTS complex formed filamentous structures in the presence of Mg2+ and ATP at the protein concentration above 3.0 mg/ml. This filament formation was reversible. The MTTS filament was dissociated to the complex by dilution to the protein concentration of 0.2 mg/ml, even in the presence of Mg2+ and ATP. The MTTS complex exhibited weak ATPase activity with the hydrolysis rate of 74 mol of ATP hydrolysis/mol of MTTS complex/min at 70 degreesC. The MTTS complex promoted the refolding of chemically denatured thermophilic archaeal citrate synthase and glucose dehydrogenase at 50 degreesC in an ATP-dependent fashion. The analysis of nucleotide specificity of chaperone activity of MTTS suggested that it was coupled with hydrolysis of ATP, CTP, or UTP.
Development and Evaluation of Quality Control Dried Blood Spot Materials in Newborn Screening for Lysosomal Storage Disorders (2008)

Suitable QC materials for newborn screening of LSDs were developed for laboratories performing DBS LSD screening. Good material linearity was observed, with goodness-of-fit values of 0.953 and higher. The QC materials may be used by screening laboratories that perform LSD analysis by MS and/or more conventional fluorescence-based screening methods.
Low-fat pointers (2013)

Referencing outside the bounds of an array or buffer is a common source of bugs and security vulnerabilities in today's software. We can enforce spatial safety and eliminate these violations by inseparably associating bounds with every pointer (fat pointer) and checking these bounds on every memory access. By further adding hardware-managed tags to the pointer, we make them unforgeable. This, in turn, allows the pointers to be used as capabilities to facilitate fine-grained access control and fast security domain crossing. Dedicated checking hardware runs in parallel with the processor's normal datapath so that the checks do not slow down processor operation (0% runtime overhead). To achieve the safety of fat pointers without increasing program state, we compactly encode approximate base and bound pointers along with exact address pointers for a 46b address space into one 64-bit word with a worst-case memory overhead of 3%. We develop gate-level implementations of the logic for updating and validating these compact fat pointers and show that the hardware requirements are low and the critical paths for common operations are smaller than processor ALU operations. Specifically, we show that the fat-pointer check and update operations can run in a 4 ns clock cycle on a Virtex 6 (40nm) implementation while only using 1100 6-LUTs or about the area of a double-precision, floating-point adder.
An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger (2010)

Group I self-splicing ribozymes commonly function as components of selfish mobile genetic elements. We identified an allosteric group I ribozyme, wherein self-splicing is regulated by a distinct riboswitch class that senses the bacterial second messenger c-di-GMP. The tandem RNA sensory system resides in the 5' untranslated region of the messenger RNA for a putative virulence gene in the pathogenic bacterium Clostridium difficile. c-di-GMP binding by the riboswitch induces folding changes at atypical splice site junctions to modulate alternative RNA processing. Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators.
Synthesis of Cobalamin−Biotin Conjugates That Vary in the Position of Cobalamin Coupling. Evaluation of Cobalamin Derivative Binding to Transcobalamin II (1996)

Six cobalamin-biotin conjugates have been prepared. The cobalamin-biotin conjugates were prepared to evaluate the effect that the location of attachment had on the binding with transcobalamin II (TCII), the cobalamin binding protein in plasma, and to evaluate their potential use for in vitro and in vivo applications. This study focused only on the effect of binding with TCII. To decrease the possibility of steric problems in binding of the cobalamin conjugates with TCII, and biotin's binding with streptavidin or avidin, moieties of 11-18 atoms in length were used as linkers. Four biotin conjugates were prepared which were attached to the corrin ring of the cobalamin molecule (on b-, c-, d-, and e-side chains). One conjugate was attached to the 5'-OH of the ribose moiety, and another conjugate was attached at the cobalt metal (in place of the cyanide moiety of cyanocobalamin). Competitive binding studies were conducted where various amounts of the cobalamin-biotin conjugates and their precursor cobalamin derivatives competed with [57Co]cyanocobalamin for binding of recombinant human TCII (rhTCII). Evaluation of cobalamin derivatives which were conjugated at the 5'-OH of ribose or the cobalt metal center indicated that conjugation at either of these positions had little effect on binding with rhTCII. However, conjugates where the attachment was made on the corrin ring substituents had a large variation in binding with rhTCII. Conjugates on the e-propionamide side chain had little effect (relative affinity was equal to or decreased less than a factor of 3) on binding with rhTCII, conjugates of the b-isomer had decreased binding (relative affinity decreased less than a factor of 10), conjugates of the d-propionamide had further decreased binding (relative affinity decreased between 44 and 69 times), and conjugates on the c-acetamide group had poor binding to rhTCII (relative affinity decreased between 295 and 1160 times). The significance of the side chains on the corrin ring in providing specificity and high-affinity binding with rhTCII is discussed.
[Possibilities and limitations of thrombelastometry/-graphy]. (2006)

Thrombelastometry/-graphy provides information about clot strength and stability. Modified thrombelastometry/-graphy improved standardisation and diagnostic information using this system. Heparinase modified thrombelastometry/-graphy allows estimation of heparin. The introduction of FIBTEM on the ROTEM first allows a clear estimation of the plasmatic and the platelet component of clot strength, which may be of interest in managing haemostasis in perioperative setting. In this context the meaning of fibrinogen should be evaluated. As our clinical data show there is no predictive value of elevated D-dimers to hyperfibrinolysis in perioperative setting. However, thrombelastometry/-graphy do not deteckt disturbances in primary haemostasis such as von Willebrand Syndrom. The effect of acetylsalicylacid and clopidogrel do not have any influence on thrombelastometry/-graphy, as well. GPIIb/IIIa-Antagonists such as ReoPro may reduce clot strength at high dosis. A similar effect may be expected in severe M. Glanzmann. The correlation between coagulation time in thrombelastometry/-graphy (CT/r-value) to conventional coagulation may be low because of different activators used. The introduction of rotationthrombelastometry (ROTEM) provides a stable system suitable for bedside-monitoring.
The von Hippel-Lindau tumor-suppressor gene product forms a stable complex with human CUL-2, a member of the Cdc53 family of proteins (1997)

The inactivation of the von Hippel-Lindau (VHL) gene predisposes affected individuals to VHL syndrome and is an early genetic event associated with sporadic renal cell carcinoma and CNS hemangioblastomas. The VHL protein (pVHL) has been shown to form a stable complex with elongin B and elongin C, two factors that stabilize and activate the transcription elongation factor elongin A. Here, Hs-CUL-2, a member of the recently identified multigene family, the cullins, is shown to specifically associate with the trimeric pVHL-elongin B-C (VBC) complex in vitro and in vivo. Nearly 70% of naturally occurring cancer-predisposing mutations of VHL disrupt this interaction. The pVHL-Hs-CUL-2 association is strictly dependent on the integrity of the trimeric VBC complex. Immunofluorescence studies show Hs-CUL-2 to be a cytosolic protein that can be translocated to the nucleus by pVHL. Recently it has been shown that a yeast Hs-CUL-2 homolog, Cdc53, is part of a ubiquitin protein ligase complex that targets cell cycle proteins for degradation by the ubiquitin proteolytic pathway. In Caenorhabditis elegans, a null mutation of another Hs-cul-2 homolog, Ce-cul-1, results in hyperplasia in all tissues and is required for cell cycle exit. Hence, Hs-cul-2 may be required for VHL function and, therefore, may be a candidate human tumor-suppressor gene.
T Cell Responses to HLA-A*0201-Restricted Peptides Derived from Human α Fetoprotein (2001)

Abstract α fetoprotein (AFP)-derived peptide epitopes can be recognized by human T cells in the context of MHC class I. We determined the identity of AFP-derived peptides, presented in the context of HLA-A*0201, that could be recognized by the human (h) T cell repertoire. We screened 74 peptides and identified 3 new AFP epitopes, hAFP137–145, hAFP158–166, and hAFP325–334, in addition to the previously reported hAFP542–550. Each possesses two anchor residues and stabilized HLA-A*0201 on T2 cells in a concentration-dependent class I binding assay. The peptides were stable for 2–4 h in an off-kinetics assay. Each peptide induced peptide-specific T cells in vitro from several normal HLA-A*0201 donors. Importantly, these hAFP peptide-specific T cells also were capable of recognizing HLA-A*0201+/AFP+ tumor cells in both cytotoxicity assays and IFN-γ enzyme-linked immunospot assays. The immunogenicity of each peptide was tested in vivo with HLA-A*0201/Kb-transgenic mice. After immunization with each peptide emulsified in CFA, draining lymph node cells produced IFN-γ on recognition of cells stably transfected with hAFP. Furthermore, AFP peptide-specific T cells could be identified in the spleens of mice immunized with dendritic cells transduced with an AFP-expressing adenovirus (AdVhAFP). Three of four AFP peptides could be identified by mass spectrometric analysis of surface peptides from an HLA-A*0201 human hepatocellular carcinoma (HCC) cell line. Thus, compelling immunological and physiochemical evidence is presented that at least four hAFP-derived epitopes are naturally processed and presented in the context of class I, are immunogenic, and represent potential targets for hepatocellular carcinoma immunotherapy.
SPEC hashing: Similarity preserving algorithm for entropy-based coding (2010)

Searching approximate nearest neighbors in large scale high dimensional data set has been a challenging problem. This paper presents a novel and fast algorithm for learning binary hash functions for fast nearest neighbor retrieval. The nearest neighbors are defined according to the semantic similarity between the objects. Our method uses the information of these semantic similarities and learns a hash function with binary code such that only objects with high similarity have small Hamming distance. The hash function is incrementally trained one bit at a time, and as bits are added to the hash code Hamming distances between dissimilar objects increase. We further link our method to the idea of maximizing conditional entropy among pair of bits and derive an extremely efficient linear time hash learning algorithm. Experiments on similar image retrieval and celebrity face recognition show that our method produces apparent improvement in performance over some state-of-the-art methods.
DETERMINANTS OF EMERGING MARKETSâ€™ COMMERCIAL BANK STOCK RETURNS (2010)

Although banks are central to the economic development and growth of emerging markets (Benston, 2004), most studies have not investigated the determinants of stock returns of this sector in these countries. This study, contributes to the literature in finance by investigating and identifying factors that investors should be concerned about while deciding about their investments in commercial banks in emerging markets. Our results indicate that apart from fundamental risk factors like size and price to book, duration gap, bank concentration, corruption, debt servicing socio-economic conditions, and percapita GDP also influence returns of commercial banks in emerging markets.
Crypto-Nets: Neural Networks over Encrypted Data (2014)

The problem we address is the following: how can a user employ a predictive model that is held by a third party, without compromising private information. For example, a hospital may wish to use a cloud service to predict the readmission risk of a patient. However, due to regulations, the patient's medical files cannot be revealed. The goal is to make an inference using the model, without jeopardizing the accuracy of the prediction or the privacy of the data. To achieve high accuracy, we use neural networks, which have been shown to outperform other learning models for many tasks. To achieve the privacy requirements, we use homomorphic encryption in the following protocol: the data owner encrypts the data and sends the ciphertexts to the third party to obtain a prediction from a trained model. The model operates on these ciphertexts and sends back the encrypted prediction. In this protocol, not only the data remains private, even the values predicted are available only to the data owner. Using homomorphic encryption and modifications to the activation functions and training algorithms of neural networks, we show that it is protocol is possible and may be feasible. This method paves the way to build a secure cloud-based neural network prediction services without invading users' privacy.
Categorical meta-analysis of Osteopontin as a clinical cancer marker (2010)

Although extensive literature exists on cancer biomarkers few have found entry into clinical use. In particular, the cancer metastasis gene Osteopontin has been investigated extensively but it has not yet been applied to routine diagnostics. Here, we conduct a meta-analysis of data from the published literature and from RNA microarrays deposited in Oncomine. Osteopontin has been associated with 34 cancers. It is a marker for breast, cervical, colorectal, head and neck, liver, lung, ovarian and prostate cancers, as well as for sarcoma. Osteopontin is overexpressed in the metastases of colorectal cancers, lung cancers and melanomas, but not in ovarian cancer. Further, Osteopontin is indicative of the underlying mechanism of transformation only in certain virally induced tumors, where its function as a TH1 cytokine likely plays important roles. These results refine the value of Osteopontin as a cancer biomarker.
Combined in Vitro Transcription and Reverse Transcription to Amplify and Label Complex Synthetic Oligonucleotide Probe Libraries (2015)

Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection-based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotide library is amplified by transcription to create an RNA library. Next, dye- or hapten-conjugate primers are used to reverse transcribe the RNA to produce a dye-labeled cDNA library. Finally the RNA is hydrolyzed under alkaline conditions to obtain the single-stranded fluorescent probes library. Starting from unique oligonucleotide library constructs, we present two methods to produce single-stranded probe libraries. The two methods differ in the type of reverse transcription (RT) primer, the incorporation of fluorescent dye, and the purification of fluorescent probes. The first method employs dye-labeled reverse transcription primers to produce multiple differentially single-labeled probe subsets from one microarray library. The fluorescent probes are purified from excess primers by oligonucleotide-bead capture. The second method uses an RNA:DNA chimeric primer and amino-modified nucleotides to produce amino-allyl probes. The excess primers and RNA are hydrolyzed under alkaline conditions, followed by probe purification and labeling with amino-reactive dyes. The fluorescent probes created by the combination of transcription and reverse transcription can be used for FISH and to detect any RNA and DNA targets via hybridization.
Semi-Supervised Recursive Autoencoders for Predicting Sentiment Distributions (2011)

We introduce a novel machine learning frame-work based on recursive autoencoders for sentence-level prediction of sentiment label distributions. Our method learns vector space representations for multi-word phrases. In sentiment prediction tasks these represen-tations outperform other state-of-the-art ap-proaches on commonly used datasets, such as movie reviews, without using any pre-defined sentiment lexica or polarity shifting rules. We also evaluate the model’s ability to predict sentiment distributions on a new dataset based on confessions from the experience project. The dataset consists of personal user stories annotated with multiple labels which, when aggregated, form a multinomial distribution that captures emotional reactions. Our al-gorithm can more accurately predict distri-butions over such labels compared to several competitive baselines. 1
Applied Numerical Methods With Software (1991)

Major sources of errors in numerical methods polynomial interpolation solution of nonlinear equations numerical integration numerical differentiation numerical linear algebra computations of matrix eigenvalues curve fitting to measured data initial value problems of ordinary differential equations boundary value problems of ordinary differential equations elliptic partial differential equations parabolic partial differential equations hyperbolic partial differential equations.
Pivotal role of CEACAM1 protein in the inhibition of activated decidual lymphocyte functions (2002)

Lymphocytes in direct contact with embryonic extravillous trophoblasts constitute more than 40% of decidual cells and appear to play major roles in implantation and early gestation. A unique subset of NK cells, making up 70-80% of decidual lymphocytes, express high levels of CD56 but lack CD16. We have recently demonstrated a novel class I MHC-independent inhibitory mechanism of NK cell cytotoxicity that is mediated by CEACAM1 homotypic interactions. This mechanism is used by some melanoma cells to avoid attack, mainly by CD16(-) NK cells. We now demonstrate that CEACAM1 is expressed on primary extravillous trophoblasts and is upregulated on the vast majority of IL-2-activated decidual lymphocytes, including NK, T, and NKT cells. Importantly, we present evidence that CEACAM1 interactions inhibit the lysis, proliferation, and cytokine secretion of activated decidual NK, T, and NKT cells, respectively. In vivo analysis of decidual lymphocytes isolated from cytomegalovirus-infected (CMV-infected) pregnant women revealed a dramatic increase in the expression of CEACAM1. Finally, we suggest that a novel ligand for this adhesion molecule is present on the surface of CMV-infected fibroblasts. These combined results demonstrate a major role for the CEACAM1 protein in controlling local decidual immune responses.
Immersive 3D modeling with Blender and off-the-shelf hardware (2013)

We present an immersive 3D modeling application with stereoscopic graphics, head tracking, and 3D input devices. The application was built in three weeks on top of Blender, an open source 3D modeling software, and relies solely on affordable, off-the-shelf hardware like PlayStation Move controllers. Our goal was to create an easy to use 3D modeling environment that employs both 2D and 3D interaction techniques and contains several modeling tools. We conducted a basic user study where novice and professional 3D artists created 3D models with our application. The study participants thought that the application was fun and intuitive to use, but accurate posing of objects was difficult. We also examined the participants' beliefs about future use of immersive technology in 3D modeling. The short implementation time of the application, its many features, and the 3D models created by the study participants set an example of what can be achieved with open source software and off-the-shelf hardware.
Handcrafting textile interfaces from a kit-of-no-parts (2010)

This paper explores the idea of handcrafted electronics. We introduce a kit-of-no-parts approach to building electronics from a diverse palette of craft materials, which we argue is more personal, understandable and accessible than the construction of technology from a kit of pre-determined components. We illustrate our approach by describing the design, construction, and dissemination of a collection of textile sensors, and detailing a website and a series of workshops through which we share our approach.
Design and implementation of the CALO query manager (2006)

Serum TTR level is suggested to be associated with cognitive scores in people with NC and to be an indicator of progression from NC to MCI.