gebhart/patrepeval huggingface dataset:
The nuclear envelope protein Nesprin-2 has roles in cell proliferation and differentiation during wound healing (2012)

Nesprin-2, a type II transmembrane protein of the nuclear envelope, is a component of the LINC complex that connects the nuclear lamina with the actin cytoskeleton. To elucidate its physiological role we studied wound healing in Nesprin-2 Giant deficient mice and found that a loss of the protein affected wound healing particularly at later stages during fibroblast differentiation and keratinocyte proliferation leading to delayed wound closure. We identified altered expression and localization of transcription factors as one of the underlying mechanisms. Furthermore, the actin cytoskeleton which surrounds the nucleus was altered and keratinocyte migration was slowed down and focal adhesion formation enhanced. We also uncovered a new activity of Nesprin-2. When we probed for an interaction of Nesprin-2 Giant with chromatin we observed in ChIP Seq experiments an association of the protein with heterochromatic and centromeric DNA. Through this activity Nesprin-2 can affect the nuclear landscape and gene regulation. Our findings suggest functions for Nesprin-2 at the nuclear envelope (NE) in gene regulation and in regulation of the actin cytoskeleton which impact on wound healing.
Network locality at the scale of processes (1991)

Packets on a LAN can be viewed as a series of references to and from the objects they address.
A positioning QA procedure for 2D/2D (kV/MV) and 3D/3D (CT/CBCT) image matching for radiotherapy patient setup (2009)

A positioning QA procedure for Varian's 2D/2D (kV/MV) and 3D/3D (planCT/CBCT) matching was developed. The procedure was to check: (1) the coincidence of on-board imager (OBI), portal imager (PI), and cone beam CT (CBCT)'s isocenters (digital graticules) to a linac's isocenter (to a pre-specified accuracy); (2) that the positioning difference detected by 2D/2D (kV/MV) and 3D/3D(planCT/CBCT) matching can be reliably transferred to couch motion. A cube phantom with a 2 mm metal ball (bb) at the center was used. The bb was used to define the isocenter. Two additional bbs were placed on two phantom surfaces in order to define a spatial location of 1.5 cm anterior, 1.5 cm inferior, and 1.5 cm right from the isocenter. An axial scan of the phantom was acquired from a multislice CT simulator. The phantom was set at the linac's isocenter (lasers); either AP MV/R Lat kV images or CBCT images were taken for 2D/2D or 3D/3D matching, respectively. For 2D/2D, the accuracy of each device's isocenter was obtained by checking the distance between the central bb and the digital graticule. Then the central bb in orthogonal DRRs was manually moved to overlay to the off-axis bbs in kV/MV images. For 3D/3D, CBCT was first matched to planCT to check the isocenter difference between the two CTs. Manual shifts were then made by moving CBCT such that the point defined by the two off-axis bbs overlay to the central bb in planCT. (PlanCT can not be moved in the current version of OBI1.4.) The manual shifts were then applied to remotely move the couch. The room laser was used to check the accuracy of the couch movement. For Trilogy (or Ix-21) linacs, the coincidence of imager and linac's isocenter was better than 1 mm (or 1.5 mm). The couch shift accuracy was better than 2 mm.
Cation‐binding cyclic peptides with lipophilic tails (1979)

Abstract We have synthesized and characterized a series of cation‐binding cyclic octapeptides which may function as potential ionophoric substances. The materials contain varying degrees of hydrophobic character, which was controlled systematically through the incorporation of N ‐alkylglycine residues where N ‐alkyl = methyl, n ‐hexyl, cyclohexyl, or n ‐decyl. The peptides reported include cyclo(Phe‐Sar‐Gly‐Sar) 2 , cyclo(Glu(OBzl)‐Sar‐Gly‐Sar‐Glu(OBzl)‐Sar‐Gly‐( N ‐decyl)Gly), cyclo(Glu(OBzl)‐Sar‐Gly‐( N ‐decyl)Gly) 2 , cyclo(Glu(OBzl)‐Sar‐Gly‐( N ‐hexyl)Gly) 2 , cyclo(Glu(OBzl)‐Sar‐Gly‐( N ‐cyclohexyl)Gly) 2 , and the corresponding free diacid forms of the Glu‐containing compounds. Using 13 C‐ and 1 H‐nmr spectra, we demonstrated that the mixture of cis / trans peptide bond‐isomer conformers, characteristic of the free‐peptide benzyl esters in solution, was converted to unique C 2 ‐symmetric, presumably all‐ trans conformers on complexation with calcium ions. Cation‐transport experiments, using the thick‐liquid model of transport in a Pressman cell, established that these compounds transport a variety of cations and that one peptide examined in detail, cyclo(Glu(OBzl)‐Sar‐Gly‐( N ‐decyl)Gly) 2 (selectivity Ca 2+ > Na + > K + > Mn 2+ > Cu 2+ > Mg 2+ > Co 2+ > Zn 2+ ), transports calcium about an order of magnitude more efficiently than magnesium.
Effectiveness of edible coatings to inhibit browning and inactivate foodborne pathogens on fresh‐cut apples (2020)

Abstract Multiple formulations of edible coating solutions were developed and evaluated for their ability to maintain the quality and minimize populations of foodborne bacteria on fresh‐cut apples. Fresh‐cut apples were artificially inoculated with Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes , and dip‐treated with coating solutions. Changes in populations of pathogens and molds and yeasts (M&Y) were evaluated after solution treatments and during storage at 4°C for 35 days. Changes in color, texture firmness, and weight loss during storage were also determined. Among the formulations, the solution containing 1% of three organic acids (acetic, lactic, and levulinic acids), 2% N‐acetyl‐l‐cysteine or L‐cysteine with 0.5% chitosan demonstrated the best effectiveness for the simultaneous reduction of pathogenic and spoilage microorganisms, control of browning, and maintenance of the quality of fresh‐cut apples. The treated apple slices had nondetectable pathogens and M&Y (<1 log CFU) and the least quality changes for 35‐day storage. The developed solutions can be used at processing plants, retail stores, or homes to protect fresh‐cut apples or other fresh‐cut fruits and vegetables from microbiological and quality deterioration.
Distributed shared abstractions (DSA) on multiprocessors (1996)

Any parallel program has abstractions that are shared by the program's multiple processes. Such shared abstractions can considerably affect the performance of parallel programs, on both distributed and shared memory multiprocessors. As a result, their implementation must be efficient, and such efficiency should be achieved without unduly compromising program portability and maintainability. The primary contribution of the DSA library is its representation of shared abstractions as objects that may be internally distributed across different nodes of a parallel machine. Such distributed shared abstractions (DSA) are encapsulated so that their implementations are easily changed while maintaining program portability across parallel architectures. The principal results presented are: a demonstration that the fragmentation of object state across different nodes of a multiprocessor machine can significantly improve program performance; and that such object fragmentation can be achieved without compromising portability by changing object interfaces. These results are demonstrated using implementations of the DSA library on several medium scale multiprocessors, including the BBN Butterfly, Kendall Square Research, and SGI shared memory multiprocessors. The DSA library's evaluation uses synthetic workloads and a parallel implementation of a branch and bound algorithm for solving the traveling salesperson problem (TSP).
Polymer-Matrix Composites for Microelectronics (2001)

Polymer-matrix composite materials for microelectronics are reviewed in terms of the science and applications. They include those with continuous and discontinuous fillers in the form of particles and fibres, as designed for high thermal conductivity, low thermal expansion, low dielectric constant, high/low electrical conductivity and electromagnetic interference shielding. Applications include heat sinks, housings, printed wiring boards, substrates, lids, die attach, encapsulation, interconnections and thermal interface materials.
Human Papillomavirus Type 16 Integration in Cervical Carcinoma In Situ and in Invasive Cervical Cancer (2006)

Integration of human papillomavirus type 16 (HPV-16) into the host DNA has been proposed as a potential marker of cervical neoplastic progression. In this study, a quantitative real-time PCR (qRT-PCR) was used to examine the physical status of HPV-16 in 126 cervical carcinoma in situ and 92 invasive cervical cancers. Based on criteria applied to results from this qRT-PCR assay, HPV-16 was characterized in carcinoma in situ cases as episomal (61.9%), mixed (i.e., episomal and integrated; 29.4%), and integrated (8.7%) forms. In invasive cervical cancer samples, HPV-16 was similarly characterized as episomal (39.1%), mixed (45.7%), and integrated (15.2%) forms. The difference in the frequency of integrated or episomal status estimated for carcinoma in situ and invasive cervical cancer cases was statistically significant (P = 0.003). Extensive mapping analysis of HPV-16 E1 and E2 genes in 37 selected tumors demonstrated deletions in both E1 and E2 genes with the maximum number of losses (78.4%) observed within the HPV-16 E2 hinge region. Specifically, deletions within the E2 hinge region were detected most often between nucleotides (nt) 3243 and 3539. The capacity to detect low-frequency HPV-16 integration events was highly limited due to the common presence and abundance of HPV episomal forms. HPV-16 E2 expressed from intact episomes may act in trans to regulate integrated genome expression of E6 and E7.
Narrative text classification for automatic key phrase extraction in web document corpora (2005)

Automatic key phrase extraction is a useful tool in many text related applications such as clustering and summarization. State-of-the-art methods are aimed towards extracting key phrases from traditional text such as technical papers. Application of these methods on Web documents, which often contain diverse and heterogeneous contents, is of particular interest and challenge in the information age. In this work, we investigate the significance of narrative text classification in the task of automatic key phrase extraction in Web document corpora. We benchmark three methods, TFIDF, KEA, and Keyterm, used to extract key phrases from all the plain text and from only the narrative text of Web pages. ANOVA tests are used to analyze the ranking data collected in a user study using quantitative measures of acceptable percentage and quality value. The evaluation shows that key phrases extracted from the narrative text only are significantly better than those obtained from all plain text of Web pages. This demonstrates that narrative text classification is indispensable for effective key phrase extraction in Web document corpora.
Avoiding Reasoning Shortcuts: Adversarial Evaluation, Training, and Model Development for Multi-Hop QA (2019)

Multi-hop question answering requires a model to connect multiple pieces of evidence scattered in a long context to answer the question. In this paper, we show that in the multi-hop HotpotQA (Yang et al., 2018) dataset, the examples often contain reasoning shortcuts through which models can directly locate the answer by word-matching the question with a sentence in the context. We demonstrate this issue by constructing adversarial documents that create contradicting answers to the shortcut but do not affect the validity of the original answer. The performance of strong baseline models drops significantly on our adversarial evaluation, indicating that they are indeed exploiting the shortcuts rather than performing multi-hop reasoning. After adversarial training, the baseline's performance improves but is still limited on the adversarial evaluation. Hence, we use a control unit that dynamically attends to the question at different reasoning hops to guide the model's multi-hop reasoning. We show that this 2-hop model trained on the regular data is more robust to the adversaries than the baseline model. After adversarial training, this 2-hop model not only achieves improvements over its counterpart trained on regular data, but also outperforms the adversarially-trained 1-hop baseline. We hope that these insights and initial improvements will motivate the development of new models that combine explicit compositional reasoning with adversarial training.
Structure−Stability Relationships in Cocrystal Hydrates: Does the Promiscuity of Water Make Crystalline Hydrates the Nemesis of Crystal Engineering? (2010)

This contribution addresses the role of water molecules in crystal engineering by studying the crystal structures and thermal stabilities of 11 new cocrystal hydrates, all of which were characterized by single crystal X-ray crystallography, powder X-ray diffraction (PXRD), infrared spectroscopy (IR), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). The cocrystal hydrates can be grouped into four categories based upon thermal stability: (1) water is lost at <100 °C; (2) water is lost between 100 and 120 °C; (3) water is lost at >120 °C; (4) dehydration occurs concurrently with the melt of the cocrystal. In order to address if there is any correlation between structure and stability, the following factors were considered: type of hydrate (tunnel hydrate or isolated hydrate); number of hydrogen bond donors and acceptors; hydrogen bond distances; packing efficiency. Category 1 hydrates exhibit water molecules in tunnels. However, no structure/stability correlations exist in any of the other categories of hydrate. To complement the cocrystal hydrates reported herein, a Cambridge Structural Database (CSD) analysis was conducted in order to address the supramolecular heterosynthons that water molecules exhibit with two of the most relevant functional groups in the context of active pharmaceutical ingredients, carboxylic acids, and alcohols. The CSD analysis suggests that, unlike cocrystals, there is great diversity in the supramolecular heterosynthons exhibited by water molecules when they form hydrogen bonds with carboxylic acids or alcohols. It can therefore be concluded that the promiscuity of water molecules in terms of their supramolecular synthons and their unpredictable thermal stability makes them a special challenge in the context of crystal engineering.
Chronic Intracerebroventricular Infusion of Nociceptin/Orphanin FQ Produces Body Weight Gain by Affecting Both Feeding and Energy Metabolism in Mice (2009)

Nociceptin/orphanin FQ (N/OFQ), an endogenous ligand for opioid receptor-like 1 (ORL1), is involved in various central functions, such as pain, psychological stress, locomotor activity, learning and memory, and feeding regulation. Of these functions, the role of N/OFQ in the regulation of feeding has been suggested by the fact that the central administration of N/OFQ leads to feeding behavior. However, the manner in which N/OFQ influences body weight control and subsequent obesity is unclear. To clarify the involvement of N/OFQ in the development of obesity, we evaluated the effects of intracerebroventricular infusion of N/OFQ on food intake and body weight in C57BL/6J mice that were fed a regular chow diet or moderately high-fat (MHF) diet (32.6% kcal fat). N/OFQ significantly increased food intake and body weight both in the regular diet- and MHF diet-fed mice, and these changes were more apparent in the MHF diet-fed mice. When we performed a pair-feeding study in N/OFQ intracerebroventricularly infused mice, N/OFQ did not cause body weight gain but increased white adipose tissue weight and plasma leptin, insulin, and cholesterol levels. N/OFQ reduced rectal temperature in pair-fed mice, in keeping with decreased UCP1 mRNA expression in brown adipose tissue. These results suggest that N/OFQ contributes to the development of obesity not only by inducing hyperphagia but also by decreasing energy expenditure.
Self-Assembling Nano-Architectures Created from a Protein Nano-Building Block Using an Intermolecularly Folded Dimeric <i>de Novo</i> Protein (2015)

The design of novel proteins that self-assemble into supramolecular complexes is an important step in the development of synthetic biology and nanotechnology. Recently, we described the three-dimensional structure of WA20, a de novo protein that forms an intermolecularly folded dimeric 4-helix bundle (PDB code 3VJF ). To harness the unusual intertwined structure of WA20 for the self-assembly of supramolecular nanostructures, we created a protein nanobuilding block (PN-Block), called WA20-foldon, by fusing the dimeric structure of WA20 to the trimeric foldon domain of fibritin from bacteriophage T4. The WA20-foldon fusion protein was expressed in the soluble fraction in Escherichia coli, purified, and shown to form several homooligomeric forms. The stable oligomeric forms were further purified and characterized by a range of biophysical techniques. Size exclusion chromatography, multiangle light scattering, analytical ultracentrifugation, and small-angle X-ray scattering (SAXS) analyses indicate that the small (S form), middle (M form), and large (L form) forms of the WA20-foldon oligomers exist as hexamer (6-mer), dodecamer (12-mer), and octadecamer (18-mer), respectively. These findings suggest that the oligomers in multiples of 6-mer are stably formed by fusing the interdigitated dimer of WA20 with the trimer of foldon domain. Pair-distance distribution functions obtained from the Fourier inversion of the SAXS data suggest that the S and M forms have barrel- and tetrahedron-like shapes, respectively. These results demonstrate that the de novo WA20-foldon is an effective building block for the creation of self-assembling artificial nanoarchitectures.
Development of a micro-fluidic manifold for copper monitoring utilising chemiluminescence detection (2004)

The progressive development of a micro-fluidic manifold for the chemiluminescent detection of copper in water samples, based on the measurement of light emitted from the Cu(ii) catalysed oxidation of 1,10-phenanthroline by hydrogen peroxide, is reported. Micro-fluidic manifolds were designed and manufactured from polymethylmethacrylate (PMMA) using three micro-fabrication techniques, namely hot embossing, laser ablation and direct micro-milling. The final laser ablated design incorporated a reagent mixing channel of dimensions 7.3 cm in length and 250 x 250 microm in width and depth (triangular cross section), and a detection channel of 2.1 cm in length and 250 x 250 microm in width and depth (total approx. volume of between 16 to 22 microL). Optimised reagents conditions were found to be 0.07 mM 1,10-phenanthroline, containing 0.10 M cetyltrimethylammonium bromide and 0.075 M sodium hydroxide (reagent 1 delivered at 0.025 mL min(-1)) and 5% hydrogen peroxide (reagent 2 delivered at 0.025 mL min(-1)). The sample stream was mixed with reagent 1 in the mixing channel and subsequently mixed with reagent 2 at the start of the detection channel. The laser ablated manifold was found to give a linear response (R(2) = 0.998) over the concentration ranges 0-150 microg L(-1) and be reproducible (% RSD = 3.4 for five repeat injections of a 75 microg L(-1) std). Detection limits for Cu(ii) were found to be 20 microg L(-1). Selectivity was investigated using a copper selective mini-chelating column, which showed common cations found in drinking waters did not cause interference with the detection of Cu(ii). Finally the optimised system was successfully used for trace Cu(ii) determinations in a standard reference freshwater sample (SRM 1640).
Analysis of epitope structure of PSP94 (prostate secretory protein of 94 amino acids): (I) immuno‐dominant and immuno‐recessive area (1997)

PSP94 is a potential biomarker for evaluating patients with prostate carcinoma. We have systematically studied the epitope structure of PSP94 by using a polyclonal antibody against human PSP94. Results of peptide mapping and ELISA tests of dose response to rabbit antiserum against human PSP94 protein showed that only the N-terminal peptides (N30 and M23) are immunoreactive while all the synthetic peptides (C28, C10) located closer to the C-terminus are completely devoid of antigenic activity with the polyclonal antibody. These results were confirmed by analysis of reciprocal competitive binding of PSP94 polyclonal antibody by the N-terminal peptides (N30 and M23) v. either recombinant GST-PSP94 fusion protein, purified recombinant PSP94, or natural PSP94 protein. To further delineate the antigenic activity of the N- and C-termini, we have also expressed N- and C-terminal half of the whole PSP94 (each 47 peptides) using the E. coli GST expression system. The recombinant N47/C47 peptides were released by thrombin cleavage from the GST fusion protein and characterized by Western blotting experiments. Dose response of the recombinant GST-PSP-N47 and -C47 peptides to PSP94 polyclonal antibody showed differential binding activities. Competitive binding of these recombinant N47/C47 proteins against the GST-PSP94 protein demonstrates that the polyclonal antibody has a higher affinity for the N47 peptide than the C47 peptide. Based on the immunological studies of both synthetic peptides and recombinant PSP94- N/C terminal proteins, we propose an epitope structure of human PSP94 with an immno-dominant N-terminus and an immuno-recessive C-terminus. J. Cell. Biochem. 65:172–185. © 1997 Wiley-Liss, Inc.
1,4‐Hydrosilylation of Pyridine by Ruthenium Catalyst: A New Reaction and Mechanism (2011)

Making introductions: A half-sandwich Ru complex catalyzes the hydrosilylation of pyridine derivatives to produce N-silyl-3-hydropyridine through a 1,4-addition of the Si–H group (see scheme). The reversibility of the hydrosilylation was suggested based on the experimental results.
An Architecture for Flexible Web Service QoS Negotiation (2006)

The Web service selection phase is usually driven only by functional requirements. Non functional requirements, such as quality of service, should be negotiated by the service consumer and the service provider during service invocation in order to produce a contract to manage service provisioning and to monitor the actual fulfilment of negotiated SLAs. In this paper, an automated approach to Web service QoS negotiation is proposed; the negotiation is performed by a negotiation broker to which both the consumer and the service provider can notify their preferences on QoS attributes and negotiation strategies by specifying the value of a relatively small set of parameters. When consumers are unable to specify such parameters or do not trust the service provisioning platform, negotiation can also be automated only on the provider side, allowing the direct interaction of the service consumer with the broker. An architecture to support the above mentioned functionalities is also described.