Miracle-dz/UniFAR-FTUs huggingface dataset:
Binding interface prediction by combining protein–protein docking results

We developed a method called residue contact frequency (RCF), which uses the complex structures generated by the protein–protein docking algorithm ZDOCK to predict interface residues. Unlike interface prediction algorithms that are based on monomers alone, RCF is binding partner specific. We evaluated the performance of RCF using the area under the precision‐recall (PR) curve (AUC) on a large protein docking Benchmark. RCF (AUC = 0.44) performed as well as meta‐PPISP (AUC = 0.43), which is one of the best monomer‐based interface prediction methods. In addition, we test a support vector machine (SVM) to combine RCF with meta‐PPISP and another monomer‐based interface prediction algorithm Evolutionary Trace to further improve the performance. We found that the SVM that combined RCF and meta‐PPISP achieved the best performance (AUC = 0.47). We used RCF to predict the binding interfaces of proteins that can bind to multiple partners and RCF was able to correctly predict interface residues that are unique for the respective binding partners. Furthermore, we found that residues that contributed greatly to binding affinity (hotspot residues) had significantly higher RCF than other residues. Proteins 2014; 82:57–66. © 2013 Wiley Periodicals, Inc.
A Suppressor of Cytokine Signaling 1 Antagonist Enhances Antigen-Presenting Capacity and Tumor Cell Antigen-Specific Cytotoxic T Lymphocyte Responses by Human Monocyte-Derived Dendritic Cells

ABSTRACT The suppressor of cytokine signaling 1 (SOCS1) has emerged as a critical inhibitory molecule for controlling the cytokine response and antigen presentation by dendritic cells (DCs), thereby regulating the magnitude of both innate and adaptive immunity. The aim of this study was to investigate whether the SOCS1 antagonist pJAK2(1001-1013) peptide can weaken or block the inhibition function of SOCS1 in DCs by evaluating the phenotype and cytokine production, antigen-presenting, and specific T-cell-activating capacities of DCs electroporated with human gastric cancer cell total RNA. Furthermore, STAT1 activation of the JAK/STAT signal pathway mediated by SOCS1 was analyzed by Western blotting. The results demonstrate that the SOCS1 antagonist pJAK2(1001-1013) peptide upregulated the expression of the maturation marker (CD83) and costimulatory molecule (CD86) of RNA-electroporated human monocyte-derived mature DCs (mDCs), potentiated the capacity of mDCs to induce T-cell proliferation, stimulated the secretion of proinflammatory cytokines, and enhanced the cytotoxicity of tumor cell antigen-specific CTLs activated by human gastric cancer cell total RNA-electroporated mDCs. Data from Western blot analysis indicate that STAT1 was further activated in pJAK2(1001-1013) peptide-loaded mDCs. These results imply that the SOCS1 antagonist pJAK2(1001-1013) peptide is an effective reagent for the enhancement of antigen-specific antitumor immunity by DCs.
The mesenchymal stem cell–derived microvesicles enhance sciatic nerve regeneration in rat: A novel approach in peripheral nerve cell therapy

BACKGROUND The accomplishment for desired functional peripheral nerve regeneration is still challenging despite various materials and methods. The effects of local application of omental adipose mesenchymal stromal cell–derived microvesicles (MVs) on peripheral nerve regeneration were studied using a rat sciatic nerve transection model. METHODS A 10-mm gap of sciatic nerve was bridged with a chitosan conduit. The rats were divided into five experimental groups randomly as follows: cultured undifferentiated omental adipose-derived stromal cells, rest mesenchymal stem cell–derived MVs (c-MVs), anti-inflammatory mesenchymal stem cell–derived MVs (anti-MVs), proinflammatory mesenchymal stem cell–derived MVs (pro-MVs), and negative control (Chit). RESULTS The functional assessment of nerve regeneration (walking track analyses), electrophysiologic measurements, muscle mass measurements, as well as histomorphometrical and immunohistochemical indices showed drastic improvement in nerve regeneration in c-MVs and anti-MVs animals compared with pro-MVs animals (p < 0.05). CONCLUSION The anti-inflammatory stem cell–derived MVs can be used as an alternative for the improvement of rat sciatic nerve regeneration.
A General Memory-Bounded Learning Algorithm

Designing bounded-memory algorithms is becoming increasingly important nowadays. Previous works studying bounded-memory algorithms focused on proving impossibility results, while the design of bounded-memory algorithms was left relatively unexplored. To remedy this situation, in this work we design a general bounded-memory learning algorithm, when the underlying distribution is known. The core idea of the algorithm is not to save the exact example received, but only a few important bits that give sufficient information. This algorithm applies to any hypothesis class that has an "anti-mixing" property. This paper complements previous works on unlearnability with bounded memory and provides a step towards a full characterization of bounded-memory learning.
Refinement of the structure of recombinant rat intestinal fatty acid-binding apoprotein at 1.2-A resolution.

The three-dimensional structure of the 131-residue rat intestinal fatty acid-binding protein, without bound ligand (apoI-FABP), has been refined with x-ray diffraction data to a nominal resolution of 1.19 A. The final model has a conventional crystallographic R-factor of 16.9% for 34,290 unique reflections [a root mean square (r.m.s.) deviation for bond length of 0.012 A and a r.m.s. deviation of 2.368 degrees for bond angles]. Ninety-two residues are present as components of the protein's 10 anti-parallel beta-strands while 14 residues are part of its two short alpha-helices. The beta-strands and alpha-helices are organized into two nearly orthogonal beta-sheets. Particular attention has been placed in defining solvent structure and the structures of discretely disordered groups in this protein. Two hundred thirty-seven solvent molecules have been identified; 24 are located within apoI-FABP. The refined model includes alternate conformers for 228 protein atoms (109 main-chain, 119 side-chain) and 63 solvent molecules. We have found several aromatic side-chains with multiple conformations located near, or in, the protein's ligand binding site. This observation, along with the fact that these side-chains have a temperature factor that is relatively higher than that of other aromatic residues, suggests that they may be involved in the process of noncovalent binding of fatty acid. The absence of a true hydrophobic core in I-FABP suggests that its structural integrity may be maintained primarily by a hydrogen bonding network involving protein and solvent atoms.
Plasminogen Activator Inhibitor‐1 Controls Bone Marrow‐Derived Cells Therapeutic Effect Through MMP9 Signaling: Role in Physiological and Pathological Wound Healing

We assessed the role of plasminogen activator inhibitor‐1 (PAI‐1) and matrix metalloproteinase 9 (MMP9) in wound healing process and in the bone marrow mononuclear cells (BMMNC)‐related effects on physiological and pathological wound healing. A full thickness excision wound was created by removal of the skin on the midback of irradiated and nonirradiated animals. Angiogenesis and re‐epithelialization were markedly increased in PAI‐1−/− mice compared to wild‐type (WT) animals. We revealed high MMP activity in tissue of PAI‐1−/− animals. Of interest, the wound healing process was reduced in PAI‐1−/−:MMP9−/− animals compared to PAI‐1−/− mice, suggesting a key role of MMP9 in beneficial effect of PAI‐1 deficiency on wound closure. To unravel the role of PAI‐1 in BMMNC relative effects, mice were treated with or without local injection of BMMNC isolated from WT, PAI‐1−/−, and PAI‐1−/−: MMP9−/− animals for 14 days (106 cells, n = 6 per group). In WT nonirradiated mice, transplantation of BMMNC isolated from PAI‐1−/− animals enhanced wound formation when compared with WT BMMNC. BMMNC differentiation into cells with endothelial phenotype was enhanced by PAI‐1 deficiency. These effects were abrogated in PAI‐1−/−:MMP9−/− and MMP9−/− BMMNC. In addition, using chimeric mice, we demonstrated that PAI‐1 deficiency environment increased the BMMNC‐GFP recruitment to the wound site, whereas this effect was abrogated when using PAI‐1−/−:MMP9−/− BMMNC. PAI‐1 deficiency, at least through MMP9 upregulation, enhanced wound healing and BMMNC therapeutic potential in irradiated and nonirradiated animals. Stem Cells2012;30:1436–1446
Golden Rule of Morphology and Variants of Word forms

Abstract In many languages, some words can be written in several ways. We call them variants. Values of all their morphological categories are identical, which leads to an identical morphological tag. Together with the identical lemma, we have two or more wordforms with the same morphological description. This ambiguity may cause problems in various NLP applications. There are two types of variants – those affecting the whole paradigm (global variants) and those affecting only wordforms sharing some combinations of morphological values (inflectional variants). In the paper, we propose means how to tag all wordforms, including their variants, unambiguously. We call this requirement “Golden rule of morphology”. The paper deals mainly with Czech, but the ideas can be applied to other languages as well.
Rent-sharing in the multi-fibre arrangement : evidence from U.S. - Hong Kong trade in apparel

The Multi-Fibre Arrangement (MFA) restricts the access of developing country exporters to developed country markets. It is usually assumed that the exporting countries receive all of the economic rents that result from these import restrictions - making it unclear whether the developing countries gain or lose as a result of the MFA. Recent theoretical work on trade policy under imperfect competition casts doubt on whether exporting countries receive all of the quota rents arising from voluntary export restraints such as those applied by the MFA. Drawing on this theoretical literature, Erzan, Krishna, and Tan (1991) tested and rejected the hypothesis that MFA quota rents on exports from Hong Kong to the United States accrued in full to the Hong Kong exporters. The results in this paper build on that hypothesis-testing analysis and assess its implications for the returns to Hong Kong producers. Their results suggest that rent sharing is an extremely important feature of the market for apparel exports from Hong Kong. U.S. importers were estimated to receive rents that were about 62 percent of the landed price of the imports. The authors conclude that the total potential rents arising from the MFA were split unevenly between the U.S. and Hong Kong - with the U.S. share ranging from 47 percent for skirts to 94 percent for playsuits. If the results of this study are corroborated for other developing countries, the implications of the MFA for developing countries are considerably worse than has typically been assumed.
Image Quality Analysis of a Novel Histogram Equalization Method for Image Contrast Enhancement

The use of image contrast enhancement has become increasingly essential due to the need to better show the visual information contained within the image for all vision-based systems. This has lead to motivation for the design of a powerful and accurate automatic contrast enhancement for a digital image. Histogram equalization is the most commonly used contrast enhancement method. However, the conventional histogram equalization methods usually result in excessive contrast enhancement, which causes the unnatural look and visual artifacts of the processed image. In this paper, we propose a novel histogram equalization method using the automatic histogram separation along with the piecewise transformed function. The contrast enhancement results of the proposed method were not only analyzed through qualitative visual inspection and for quantitative accuracy, but are also compared to the results of other state-of-the-art methods.
Sources of Motivation in Business Surveys.

Survey organizations are typically faced with – and burdened because of – nonresponse and measurement errors in business surveys. These errors are assumed not to be so much a result of actual response burden as of perceived burden. This suggests that a driving force, i.e. the motivation for participation, and accurate and timely response, is lacking. Knowledge of sources from which this motivation comes from in business surveys, promises to enhance capabilities of survey organizations to influence the response behavior. This paper seeks to identify these sources of motivation based on motivation theory on the one hand and empirical data from the Netherlands and Slovenia on the other, and suggests recommendations for increasing motivation in business surveys. These recommendations should be a useful asset for survey organizations to develop strategies to improve survey participation and response quality.
FGF‐2‐induced cell proliferation stimulates anatomical, neurophysiological and functional recovery from neonatal motor cortex injury

Infant rats treated with basic fibroblast growth factor‐2 (FGF‐2) after postnatal day (P)10 motor cortical injury, show functional improvement in adulthood relative to those that do not receive FGF‐2. In this study we used a combination of behavioural, immunohistochemical, electrophysiological, electron microscopic and teratological approaches to investigate possible mechanisms by which FGF‐2 may influence functional recovery. We show that subcutaneous injections of FGF‐2 following bilateral lesions to the motor cortex at P10 in the rat leads to filling of the lesion area with migrating neuroblasts and cycling cells. We assessed the functionality of this tissue in adulthood, and show that cells from the filled region spontaneously fire and form synapses. Behavioural analysis shows enhanced motor performance in the FGF‐2‐treated lesion rats in comparison to vehicle‐treated lesion rats, and this improvement is reversed by removal of the tissue from the previously lesioned area or by blocking cortical regeneration by embryonic treatment with bromodeoxyuridine (BrdU). The results show that FGF‐2 stimulates filling of the lesion cavity with cells after neonatal motor cortex lesions, that the new tissue has anatomical and physiological properties similar to control tissue, and that the filled region supports motor behaviour.
Stockout-Based Substitution and Inventory Planning in Textbook Retailing

We demonstrate the value of utility-based choice models to estimate demand and plan inventory for new and used textbooks in the presence of consumer choice and stockout-based substitution at a university textbook retailer. Demand information is censored, the exact time of stockout is not observed, and the short selling season often does not allow for replenishment. Using data for 26,749 book titles from 2007 to 2011 and a simulation experiment calibrated on real data, we show that an attribute-based choice model generates accurate demand estimates (mean absolute percentage error less than 1%) even when nearly 90% of the textbooks in the fit sample experience stockout. This performance is driven by the heterogeneity of product attributes and is robust to the occurrence of product returns. We implement this model at the bookstore in a controlled field experiment and obtain over 10% increase in profit. The results show that accounting for asymmetric and stockout-based substitution in demand estimation and inventory planning enables us to make systematic corrections in inventory mix and inventory level compared to the existing process.
International Society for Minimally Invasive Cardiothoracic Surgery Consensus Statements: Definitions and Terms of Reference

RATIONALE Effective evidence-based clinical guidelines can improve quality of care by decreasing inappropriate practice and improving transfer of new knowledge and technologies into practice. 1–3 As evidenced by the plethora of existing guidelines, there has been much expenditure of time and resources in creating clinical guidelines over the past two decades.4 However, the quality of these guidelines has ranged from poor to exceptional, and there has been distrust among potential users of guidelines who experience confusion as to which guidelines are reliable.1,4,17–26 The Conference on Guideline Standardization (COGS) has defined a gold standard for guideline reporting to promote guideline quality and facilitate guideline implementation.5 The standards given by the COGS were drawn primarily from the Institute of Medicine clinical guideline elements6 and from other existing instruments used for critical appraisal of clinical practice guidelines, including the AGREE instrument.7,8 Until recently, few clinical guidelines existed in the area of surgery and perioperative medicine. To mitigate this gap and to promote evidence-based practice in minimally invasive cardiothoracic surgery, the International Society for Minimally Invasive Cardiothoracic Surgery (ISMICS) has made efforts to develop international consensus statements that are based on rigorous appraisal of the best available clinical research, interjected by clinical expertise and opinion (explicitly declared as such) only when the evidence is insufficient to address the issue at hand. To date, two areas of controversy in minimally invasive cardiothoracic surgery have been addressed through ISMICS Consensus Statements: (1) off-pump coronary artery bypass grafting in lowand high-risk patients,9 and (2) endoscopic venous harvesting for coronary bypass grafting.10,11 Future consensus statements will continue to address areas of innovation or controversy of high relevance in this field. ISMICS consensus statements strive to meet all of the elements set out by COGS. The following addresses the details of the ISMICS consensus process and congruence with COGS.
Multiple Memory Systems: Evidence from Stroke

In this report, we describe the “fractionation of memory systems” in a 62-yr. -old woman following a left anterior stroke. Despite the presence of a significant, persistent declarative memory (verbal learning) deficit, this patient exhibited relatively intact procedural learning. The latter was manifested over a 4-day period by improved performance on a maze task executed under “mirror-tracing” conditions. By the final set of trials, the patient's performance approximated that of a normal control subject with respect to speed, although not errors. The selective preservation of particular learning abilities in brain-damaged patients has implications for rehabilitative interventions.
Identification of a novel serum protein secreted by lung carcinoma cells.

The murine anti-human lung tumor monoclonal antibody L3 recognizes antigens found both in the medium of cultured carcinoma cells and in normal human serum. Sequential immunoprecipitation experiments indicate that the L3 antigen is also recognized by a previously described monoclonal antibody directed against a melanoma-associated antigen [Natali, P. G. , Wilson, B. S. , Imai, K. , Bigotti, A. , & Ferrone, S. (1982) Cancer Res. 42, 583-589]. This antibody precipitated a Mr 76000 glycoprotein from metabolically labeled extracts of the lung carcinoma cell line Calu-1 and a Mr 94 000 glycoprotein from labeled culture medium. Pulse-chase experiments suggested a precursor-product relationship between these molecules. Analysis of glycosidase sensitivities of the two forms indicated that maturation of carbohydrate side chains correlated with the apparent increase in molecular weights. L3 antigenic activity, measured in a competitive radiometric cell binding assay, was purified more than 90-fold from serum-free medium of Calu-1 cells and more than 3000-fold from normal human serum. The major immunoreactive components purified from culture medium and serum were identical with respect to apparent molecular weight, electrophoretic mobility, pI, glycosidase sensitivity, and V8 protease fingerprints. In addition, the sequence of the amino-terminal 16 N-terminal amino acid residues of the major immunoreactive species from both sources was identical. The properties of the L3 antigen did not correspond to those of any known protein, suggesting that this serum protein has not been previously characterized.
Development and Application of a upp-Based Counterselective Gene Replacement System for the Study of the S-Layer Protein SlpX of Lactobacillus acidophilus NCFM

ABSTRACT In silico genome analysis of Lactobacillus acidophilus NCFM coupled with gene expression studies have identified putative genes and regulatory networks that are potentially important to this organism's survival, persistence, and activities in the gastrointestinal tract. Correlation of key genotypes to phenotypes requires an efficient gene replacement system. In this study, use of the upp-encoded uracil phosphoribosyltransferase (UPRTase) of L. acidophilus NCFM was explored as a counterselection marker to positively select for recombinants that have resolved from chromosomal integration of pORI-based plasmids. An isogenic mutant carrying a upp gene deletion was constructed and was resistant to 5-fluorouracil (5-FU), a toxic uracil analog that is also a substrate for UPRTase. A 3.0-kb pORI-based counterselectable integration vector bearing a upp expression cassette, pTRK935, was constructed and introduced into the Δupp host harboring the pTRK669 helper plasmid. Extrachromosomal replication of pTRK935 complemented the mutated chromosomal upp allele and restored sensitivity to 5-FU. This host background provides a platform for a two-step plasmid integration and excision strategy that can select for plasmid-free recombinants with either the wild-type or mutated allele of the targeted gene in the presence of 5-FU. The efficacy of the system was demonstrated by in-frame deletion of the slpX gene (LBA0512) encoding a novel 51-kDa secreted protein associated with the S-layer complex of L. acidophilus. The resulting ΔslpX mutant exhibited lower growth rates, increased sensitivity to sodium dodecyl sulfate, and greater resistance to bile. Overall, this improved gene replacement system represents a valuable tool for investigating the mechanisms underlying the probiotic functionality of L. acidophilus.