gebhart/patrepeval huggingface dataset:
<i>AbDesign</i>: An algorithm for combinatorial backbone design guided by natural conformations and sequences (2015)

Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity.
CheapStat: An Open-Source, “Do-It-Yourself” Potentiostat for Analytical and Educational Applications (2011)

Although potentiostats are the foundation of modern electrochemical research, they have seen relatively little application in resource poor settings, such as undergraduate laboratory courses and the developing world. One reason for the low penetration of potentiostats is their cost, as even the least expensive commercially available laboratory potentiostats sell for more than one thousand dollars. An inexpensive electrochemical workstation could thus prove useful in educational labs, and increase access to electrochemistry-based analytical techniques for food, drug and environmental monitoring. With these motivations in mind, we describe here the CheapStat, an inexpensive (<$80), open-source (software and hardware), hand-held potentiostat that can be constructed by anyone who is proficient at assembling circuits. This device supports a number of potential waveforms necessary to perform cyclic, square wave, linear sweep and anodic stripping voltammetry. As we demonstrate, it is suitable for a wide range of applications ranging from food- and drug-quality testing to environmental monitoring, rapid DNA detection, and educational exercises. The device's schematics, parts lists, circuit board layout files, sample experiments, and detailed assembly instructions are available in the supporting information and are released under an open hardware license.
A Robust Discretization of the Reissner-Mindlin Plate with Arbitrary Polynomial Degree (2020)

A numerical scheme for the Reissner–Mindlin plate model is proposed. The method is based on a discrete Helmholtz decomposition and can be viewed as a generalization of the nonconforming finite element scheme of Arnold and Falk [SIAM J. Numer. Anal., 26(6):1276-1290, 1989]. The two unknowns in the discrete formulation are the in-plane rotations and the gradient of the vertical displacement. The decomposition of the discrete shear variable leads to equivalence with the usual Stokes system with penalty term plus two Poisson equations and the proposed method is equivalent to a stabilized discretization of the Stokes system that generalizes the Mini element. The method is proved to satisfy a best-approximation result which is robust with respect to the thickness parameter $t$.
Search for microbial insect growth regulators. II Allosamidin, a novel insect chitinase inhibitor. (1987)

Allosamidin, a novel insect chitinase inhibitor, was isolated from the mycelium of Streptomyces sp. It showed strong inhibitory activity against the chitinases of the silkworm, Bombyx mori, in vitro, and also insecticidal activity by preventing its ecdysis in vivo.
Admiralty — The Maximum Cure Rule as a Limitation on the Maintenance and Cure Remedy — Cox v. Drano Corp (1976)

The Maximum Cure Rule as a Limitation on
Isolation and characterization of <i>Bacillus subtilis </i>CH16 strain from chicken gastrointestinal tracts for use as a feed supplement to promote weight gain in broilers (2015)

Spore-forming bacterial strains were isolated from chicken gastrointestinal tracts to develop a heat-stable feed supplement that promotes weight gain in broilers. Seven Bacillus strains having more than 90% sporulation were screened from the isolates and identified to be closely related with Bacillus subtilis and Bacillus licheniformis. Of the seven strains, B. subtilis CH16 was selected to develop a feed supplement for broilers, because it formed 100% heat-stable spores, grew rapidly at 42°C and quickly formed a biofilm. In large-scale trials in broilers (n ≥ 1150 per group), the group fed CH16 (3 × 10(6) CFU g(-1) pellet) showed higher average daily gain (ADG = 61·16) and lower food conversion ratio (FCR = 1·696) than did the group fed B. licheniformis CH22 (ADG = 57·10 and FCR = 1·792), the group fed B. subtilis HU58 (ADG = 51·90 and FCR = 1·868), BioPlus group (ADG = 59·32 and FCR = 1·807) and the control group (ADG = 56·02 and FCR = 1·880). In conclusion, CH16 spores significantly increased ADG by 9·17% and reduced FCR by 9·79% in broilers. The result supports the use of B. subtilis CH16 of chicken intestinal origin as a feed supplement that promote weight gain in broilers. Significance and impact of the study: This study reports screening of Bacillus strains isolated from chicken gastrointestinal tracts for development of a feed supplement that promote weight gain in broilers. Of the seven Bacillus isolates with high sporulation efficiency (≥90%), Bacillus subtilis CH16 strain showed the best growth and biofilm formation at body temperature of broilers (42°C). In large-scale trials in broilers (n ≥ 1150 per group), CH16 spores induced a 9·17% increase in daily weight gain (ADG) and a 9·79% reduction in FCR while the commercial BioPlus(®) YC induced only a 5·89% increase in ADG and a 3·88% reduction in FCR.
Independent component analysis for audio classification (2005)

In this paper, we explore the performance gains achieved by performing independent component analysis (ICA) decomposition on speech features obtained from a model of the early auditory system. ICA projection achieves dimensionality reduction by reducing the redundancy in the feature set (the transformed features are statistically independent). Performance is evaluated for an audio classification environment using a Gaussian mixture model (GMM) classifier and compared against the classification performance of AdaBoost, a wide-margin boosting algorithm. The new features are compared with mel-frequency cepstral coefficients (MFCC) and perceptual linear prediction (PLP) features. We also show that the ICA transformation is well suited for dimensionality reduction of auditory system-inspired features and it significantly improves the classification accuracy.
The Production and Characterization of Novel Heavy-Chain Antibodies Against the Tandem Repeat Region of MUC1 Mucin (2005)

Camelidae are known to produce immunoglobulins (Igs) devoid of light chains and constant heavy-chain domains (CH1). Antigen-specific fragments of these heavy-chain IgGs (VHH) are of great interest in biotechnology applications. This paper describes the first example of successfully raised heavy-chain antibodies in Camelus dromedarius (single-humped camel) and Camelus bactrianus (two-humped camel) against a MUC1 related peptide that is found to be an important epitope expressed in cancerous tissue. Camels were immunized against a synthetic peptide corresponding to the tandem repeat region of MUC1 mucin and cancerous tissue preparation obtained from patients suffering from breast carcinoma. Three IgG subclasses with different binding properties to protein A and G were purified by affinity chromatography. Both conventional and heavy-chain IgG antibodies were produced in response to MUC1-related peptide. The elicited antibodies could react specifically with the tandem repeat region of MUC1 mucin in an enzyme linked immunosorbant assay (ELISA). Anti-peptide antibodies were purified after passing antiserum over two affinity chromatography columns. Using ELISA, immunocytochemistry and Western blotting, the interaction of purified antibodies with different antigens was evaluated. The antibodies were observed to be selectively bound to antigens namely: MUC1 peptide (tandem repeat region), human milk fat globule membrane (HMFG), deglycosylated human milk fat globule membrane (D-HMFG), homogenized cancerous breast tissue and a native MUC1 purified from ascitic fluid. Ka values of specific polyclonal antipeptide antibodies were estimated in C. dromedarius and C. bactrianus, as 7 x 10(10) M(-1) and 1.4 x 10(10) M(-1) respectively.
Site specificity of the chorionic gonadotropin N-linked oligosaccharides in signal transduction (1989)

The role of the human chorionic gonadotropin (hCG) N-linked oligosaccharides in receptor binding and signal transduction was analyzed using site-directed mutagenesis and transfection studies. hCG derivatives with alterations at individual glycosylation sites were expressed in Chinese hamster ovary cells. Receptor binding studies showed that absence of any or all of the hCG N-linked oligosaccharides had only a minor effect on the receptor affinity of the derivatives. Similarly, absence of the N-linked oligosaccharides from the beta subunit or a single oligosaccharide from Asn-78 of alpha had no effect on the production of cAMP or on steroidogenesis. However, the absence of carbohydrate at Asn-52 of alpha decreases both the steroidogenic and cAMP responses. Furthermore, absence of this critical oligosaccharide unit on alpha unmasks differences in the two N-linked oligosaccharides on beta; the beta Asn-13 oligosaccharide but not the beta Asn-30 oligosaccharide plays a more important role in steroidogenesis. Dimers containing deglycosylated beta subunit and an alpha subunit lacking either the Asn-52 oligosaccharide or both oligosaccharides fail to stimulate cAMP or steroid formation. Moreover, these derivatives bind to receptor and behave as competitive antagonists. The use of site-directed mutagenesis was critical in uncovering site-specific functions of the hCG N-linked oligosaccharides in signal transduction and reveals the importance of the Asn-52 oligosaccharide in this process.
Potency factors in the delta‐endotoxin of <i>Bacillus thuringiensis</i> var. <i>aizawi</i> and the significance of plasmids in their control (1985)

Mutants defective in delta‐endotoxin crystal production from four closely related isolates of Bacillus thuringiensis var. aizawi with aizawi serotype crystals were as vigorous as the parents in terms of growth, extracellular protease production, sporulation and heat resistance of spores. Spores produced by mutants germinated faster than wild type spores possibly due to deficiency of protein, in the form of delta‐endotoxin in the spore coat. Acrystalliferous (cry—) mutants were not active in Galleria mellonella or Pieris brassicae larvae. Mutants with small crystals (sm cry) lost activity or gained extra activity against either one or the other host, revealing the presence of different toxicity factors. Solubilized crystals of parent isolates were composed of two major polypeptides with Mr values of 130 000 and 138 000. Sm cry mutants lost either polypeptide irrespective of which insect potency had been lost. Some cry — and some sm cry mutants had the same plasmid pattern as the parent; others lost one plasmid sometimes gaining another of different size. No consistent correlation was found between plasmid loss in mutants and any loss or increase of potency indicated by bioassays. It is concluded that the delta‐endotoxins of the isolates under investigation are composed of at least two toxins. The results suggest that genes coding for the production of toxic factors or for their expression may be carried on both the plasmids and the chromosome.
The gamma‐ray‐induced crosslinking of polyacrylamide (1986)

Abstract The gamma‐ray‐induced crosslinking of polyacrylamide was carried out under various conditions. The molecular weight of the polymer before inrradiation was found to be the most important factor for crosslinking. When polymers have low molecular weights such as 80,000, the intensity of radiation, the external pressure applied, and the water content of the polymer powder became important for crosslinking. Although the polycrylamide hydrogel can be obtained directly by irradiating the monomer, it was obtained more conveniently by the irradiation of monomer—polymer mixtures. The hydrogels obtained by the radiation with a dose of over 50 kgray, absorb water by 1000–1500 wt %.
Results of applying a non-evaporative mitigation technique to laser-initiated surface damage on fused-silica (2010)

We present results from a study to determine an acceptable CO<sub>2</sub> laser-based non-evaporative mitigation protocol for use on surface damage sites in fused-silica optics. A promising protocol is identified and evaluated on a set of surface damage sites created under ICF-type laser conditions. Mitigation protocol acceptability criteria for damage re-initiation and growth, downstream intensification, and residual stress are discussed. In previous work, we found that a power ramp at the end of the protocol effectively minimizes the residual stress (&lap;25 MPa) left in the substrate. However, the biggest difficulty in determining an acceptable protocol was balancing between low re-initiation and problematic downstream intensification. Typical growing surface damage sites mitigated with a candidate CO<sup>2</sup> laser-based mitigation protocol all survived 351 nm, 5 ns damage testing to fluences &gap;12.5 J/cm<sup>2</sup>. The downstream intensification arising from the mitigated sites is evaluated, and all but one of the sites has 100% passing downstream damage expectation values. We demonstrate, for the first time, a successful non-evaporative 10.6 m CO<sup>2</sup> laser mitigation protocol applicable to fused-silica optics used on fusion-class lasers like the National Ignition Facility (NIF).
A Proteomic Approach for Identification of Secreted Proteins during the Differentiation of 3T3-L1 Preadipocytes to Adipocytes (2002)

We have undertaken a systematic proteomic approach to purify and identify secreted factors that are differentially expressed in preadipocytes versus adipocytes. Using one-dimensional gel electrophoresis combined with nanoelectrospray tandem mass spectrometry, proteins that were specifically secreted by 3T3-L1 preadipocytes or adipocytes were identified. In addition to a number of previously reported molecules that are up- or down-regulated during this differentiation process (adipsin, adipocyte complement-related protein 30 kDa, complement C3, and fibronectin), we identified four secreted molecules that have not been shown previously to be expressed differentially during the process of adipogenesis. Pigment epithelium-derived factor, a soluble molecule with potent antiangiogenic properties, was found to be highly secreted by preadipocytes but not adipocytes. Conversely, we found hippocampal cholinergic neurostimulating peptide, neutrophil gelatinase-associated lipocalin, and haptoglobin to be expressed highly by mature adipocytes. We also used liquid chromatography-based separation followed by automated tandem mass spectrometry to identify proteins secreted by mature adipocytes. Several additional secreted proteins including resistin, secreted acidic cysteine-rich glycoprotein/osteonectin, stromal cell-derived factor-1, cystatin C, gelsolin, and matrix metalloprotease-2 were identified by this method. To our knowledge, this is the first study to identify several novel secreted proteins by adipocytes by a proteomic approach using mass spectrometry.
Identification of a synthetic nonapeptide sequence that inhibits motility in culture of a melanoma subclone that possesses a high metastatic potential. (1987)

A synthetic nonapeptide fragment of thrombin inhibits the cellular motility in culture of a human melanoma subclone that possesses a high metastatic potential in mice. Concomitant with the loss of ability to translocate in culture, these cells exhibit increases in the average length of actin cables and cellular surface area in contact with the substratum. The spreading activity is observed at a nonapeptide concentration of 1 nM within 1 hr of exposure at 37 degrees C. Pretreatment of cells with this nonapeptide does not block signal transduction through plasma membrane receptors for the following growth or differentiation factors: alpha-melanotropin (alpha-melanocyte-stimulating hormone), nerve growth factor, and transforming growth factor type beta. Results of the present study suggest an approach to cancer chemotherapy in which naturally occurring peptides from two functionally orthogonal classes may be used to perform two complementary functions: inhibition of metastasis and induction of differentiation.
Purification and characterization of formyl-coenzyme A transferase from Oxalobacter formigenes (1990)

Formyl-coenzyme A (formyl-CoA) transferase was purified from Oxalobacter formigenes by high-pressure liquid chromatography with hydrophobic interaction chromatography and by DEAE anion-exchange chromatography. The enzyme was a single entity on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel permeation chromatography (Mr, 44,000). It had an isoelectric point of 4.7. The enzyme catalyzed the transfer of CoA from formyl-CoA to either oxalate or succinate. Apparent Km and Vmax values, respectively, were 3.0 mM and 29.6 mumols/min per mg for formyl-CoA with an excess of succinate. The maximum specific activity was 2.15 mumols of CoA transferred from formyl-CoA to oxalate per min per mg of protein.
Multi-tenant Service Composition Based on Granularity Computing (2014)

As a common delivery model in cloud computing, SaaS applications are becoming increasingly popular. With the increasing of user's individual and diverse requirements, multi-tenancy has been the main delivery model for SaaS applications in future. Meanwhile, in order to adapt to the complex application development, application components had become modularization and fine-grained. Thus, new applications can be built through assembling those components quickly and agilely. So service composition for multi-tenant is the key to build application flexibly. This paper proposes a service granularity space for multi-tenant service composition based on granularity computing, which provides a semantic basis for multi-tenant service composition. The service granularity space supports the characteristic of hierarchy, inheritance, evolved correlation and versioning, effectively responding to the challenge of service composition for cloud computing SaaS applications. On the one hand, the service granularity space makes it possible to change disorder services into the hierarchy and ordered clustering services, and on the other hand, it makes it easy to develop multi-tenant SaaS applications by combining customization and evolution according to individual and diverse requirements. Our final experiments further demonstrate the feasibility and the efficiency of our proposed approaches.
On-demand transparency for improving hardware Trojan detectability (2008)

Malevolent Trojan circuits inserted by layout modifications in an IC at untrustworthy fabrication facilities are difficult to detect by traditional post-manufacturing testing. In this paper, we develop a novel low-overhead design methodology that facilitates the detection of inserted Trojan hardware in an IC through logic testing. As a byproduct, it also increases the security of the design by design obfuscation. Application of the proposed design methodology to an 8-bit RISC processor and a JPEG encoder resulted in improvement in Trojan detection probability significantly. It also obfuscated the design with verification mismatch for 90% of the verification points, while incurring moderate area, power and delay overheads.
Local production of complement proteins in rheumatoid arthritis synovium (2002)

In summary, local complement production and activation may play an important role in RA, and specific modulation and inhibition of local complement production could be an attractive therapeutic target for RA.
A method for semi-automatic grading of human blastocyst microscope images (2012)

The precise assessment of embryo viability is an extremely important factor for the optimization of IVF treatments. In order to assess embryo viability, several embryo scoring systems have been developed. However, they rely mostly on a subjective visual analysis of embryo morphological features and thus are subject to inter- and intra-observer variation. In this paper, we propose a method for image segmentation (the dividing of an image into its meaningful constituent regions) and classification of human blastocyst images with the aim of automating embryo grading. The delineation of the boundaries (segmentation) of the zona pellucida, trophectoderm (TE) and inner cell mass (ICM) were performed using advanced image analysis techniques (level set, phase congruency and fitting of ellipse methods). The fractal dimension and mean thickness of TE and ICM image texture descriptors (texture spectrum and grey-level run lengths) were calculated to characterize the main morphological features of the blastocyst with the aim of automatic grading using Support Vector Machine classifiers. The fractal dimension calculated from the delineated TE boundary provided a good indication of cell number (presented a 0.81 Pearson correlation coefficient with the number of cells), a feature closely associated with blastocyst quality. The classifiers showed different accuracy levels for each grade. They presented accuracy ranges from 0.67 to 0.92 for the embryo development classification, 0.67–0.82 for the ICM classification and 0.53–0.92 for the TE classification. The value 0.92 was the highest accuracy achieved in the tests with 73 blastocysts. Semi-automatic grading of human blastocysts by a computer is feasible and may offer a more precise comparison of embryos, reducing subjectivity and allowing embryos with apparently identical morphological scores to be distinguished.
Query-adaptive late fusion for image search and person re-identification (2015)

Feature fusion has been proven effective [35, 36] in image search. Typically, it is assumed that the to-be-fused heterogeneous features work well by themselves for the query. However, in a more realistic situation, one does not know in advance whether a feature is effective or not for a given query. As a result, it is of great importance to identify feature effectiveness in a query-adaptive manner.