Miracle-dz/UniFAR-FTUs huggingface dataset:
Polarizable Water Model for the Coarse-Grained MARTINI Force Field

Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.
Multicenter evaluation of new double-antigen sandwich enzyme immunoassay for measurement of anti-human immunodeficiency virus type 1 and type 2 antibodies

A new enzyme immunoassay (EIA), the Cobas Core Anti-HIV-1/HIV-2 EIA DAGS (also referred to as Roche DAGS), for the detection of antibodies to human immunodeficiency virus type 1 (HIV-1) and HIV-2 was evaluated in four centers. The assay is based on the double-antigen sandwich (DAGS) format, which enables the detection of all classes of antibodies. The antigens consist of recombinant proteins in their native conformation and of synthetic peptides. Of a total of 5,836 negative serum samples, including 95 samples likely to produce false reactivities, 6 were false positive, resulting in a specificity of 99.9%. None of 35 sera that were from noninfected individuals but contained p24-cross-reacting antibodies as revealed by Western blot (immunoblot) analysis were reactive by the Roche DAGS assay. In samples from individuals infected with HIV-1 group M (n = 499) and HIV-2 (n = 200), the sensitivity of the assay was 100%. Although containing antigens with sequences from subtype B only, the assay was also able to correctly identify with high optical density/cutoff ratios samples from subjects infected with HIV-1 subtype O (n = 10). In 17 of 19 seroconversion panels tested, the assay detected the presence of HIV-1 antibodies as early as another sandwich EIA. Eight of these panels were also analyzed by an indirect second-generation assay, which detected antibodies 2 to 10 days later than did the DAGS assay under evaluation. The excellent specificity and sensitivity of the new Cobas Core Anti-HIV-1/HIV-2 EIA DAGS are the result of the DAGS format as well as of the native, naturally folded form of the recombinant protein used as the gag antigen.
Digital Commons @ Trinity Digital Commons @ Trinity

Renal ischemia-reperfusion injury results in oxidative stress-induced alterations in barrier function. Activation of the mitogen-activated protein (MAP) kinase pathway during recovery from oxidative stress may be an effector of oxidant-induced tight junction reorganization. We hypothesized that tight junction composition and barrier function would be perturbed during recovery from oxidative stress. We developed a model of short-term H 2 O 2 exposure followed by recovery using Madin Darby Canine Kidney cells (MDCK II). H 2 O 2 perturbs barrier function without a significant cytotoxic effect except in significant doses. ERK-1/2 and p38, both enzymes of the MAP kinase pathway, were activated within minutes of exposure to H 2 O 2 . Transient exposure to H 2 O 2 produced a biphasic response in transepithelial electrical resistance (TER). An initial drop in TER at 6 hours was followed by a significant increase at 24 hours. Inhibition of ERK-1/2 activation attenuated the increase in TER observed at 24 hours. Expression of occludin initially decreased followed by partial recovery at 24 hours. In contrast, claudin-1 levels decreased and failed to recover at 24 hours. Claudin-2 levels markedly decreased at 24 hours; however, inhibition of ERK-1/2 activation was protective. Occludin and claudin-1 localization at the apical membrane on immunofluorescent images was fragmented at 6 hours after H 2 O 2 exposure with subsequent recovery of appropriate localization by 24 hours. MDCK II cell recovery after H 2 O 2 exposure is associated with functional and structural modification of the tight junction that are mediated in part by activation of the MAP kinase enzymes, ERK-1/2 and p38.
Angiotensin I-converting Enzyme Inhibitory Activities of Porcine Skeletal Muscle Proteins Following Enzyme Digestion

Inhibitory activities against angiotensin I-converting enzyme (ACE) of enzymatic hydrolysates of porcine skeletal muscle proteins were investigated. Myosin B, myosin, actin, tropomyosin, troponin and water-soluble proteins extracted from pork loin were digested by eight kinds of proteases, including pepsin, α-chymotrypsin, and trypsin. After digestion, hydrolysates produced from all proteins showed ACE inhibitory activities, and the peptic hydrolysate showed the strongest activity. In the case of myosin B, the molar concentration of peptic hydrolysate required to inhibit 50% of the activity increased gradually as digestion proceeded. The hydrolysates produced by sequential digestion with pepsin and α-chymotrypsin, pepsin and trypsin or pepsin and pancreatin showed weaker activities than those by pepsin alone, suggesting that ACE inhibitory peptides from peptic digestion might lose their active sequences after digestion by the second protease. However, the hydrolysates produced by sequential digestion showed stronger activities than those by α-chymotrypsin, trypsin or pancreatin alone. These results suggested that the hydrolysates of porcine meat were able to show ACE inhibitory activity, even if they were digested in vivo, and that pork might be a useful source of physiologically functional factors. (Asian-Aust. J. Anim. Sci. 2003. Vol 16, No. 3 : 417-424)
Comparison of high-speed electrical motors for a turbo circulator application

This paper introduces the analysis of three different electrical machine topologies for a special application. The machines are designed to operate with 6 kW output at 120 000 rpm. The design aspects of one squirrel cage induction motor and two permanent magnet machines are presented. The comparison of the machines include electromagnetic, thermal and mechanical analyses. The advantages and drawbacks of each topology under consideration are drawn. The comparison structure helps in selecting the suitable electrical machine topology also for other High-Speed (HS) applications.
Proximal Tubulopathy: Prime Mover and Key Therapeutic Target in Diabetic Kidney Disease

The current view of diabetic kidney disease, based on meticulously acquired ultrastructural morphometry and the utility of measuring plasma creatinine and urinary albumin, has been almost entirely focused on the glomerulus. While clearly of great importance, changes in the glomerulus are not the major determinant of renal prognosis in diabetes and may not be the primary event in the development of diabetic kidney disease either. Indeed, advances in biomarker discovery and a greater appreciation of tubulointerstitial histopathology and the role of tubular hypoxia in the pathogenesis of chronic kidney disease have given us pause to reconsider the current “glomerulocentric” paradigm and focus attention on the proximal tubule that by virtue of the high energy requirements and reliance on aerobic metabolism render it particularly susceptible to the derangements of the diabetic state. Such findings raise important issues for therapeutic advances specifically targeting the pathophysiological perturbations that develop in this part of the nephron.
An isoform of pex5p, the human PTS1 receptor, is required for the import of PTS2 proteins into peroxisomes.

Mutations in the peroxisome targeting signal (PTS) 1 receptor gene, PEX5 , are responsible for complementation group (CG) 2 of the peroxisome biogenesis disorders (PBD). Of the two reported patients in this CG, cells from PBD018 (homozygous for the missense mutation N489K) are defective in the import of PTS1 proteins into peroxisomes, as expected. However, cells from PBD005 (homozygous for the nonsense mutation R390ter) are defective in the import of both PTS1 and PTS2 proteins, suggesting that the PTS1 receptor also mediates PTS2-targeted protein import. To investigate this possibility, we characterized PEX5 expression and found that it undergoes alternative splicing, producing two transcripts, one containing (PEX5L) and one lacking (PEX5S) a 111 bp internal exon. Fibroblasts from PBD005 have greatly reduced levels of PEX5 transcript and protein as compared with PBD018. Transfection of PBD005 cells with PEX5S cDNA restores PTS1 but not PTS2 import; transfection with PXR5L cDNA restores both PTS1 and PTS2 protein import. Furthermore, transfection of PBD005 cells with PEX5L cDNAs containing the patient mutations (which are located downstream of the additional exon) restores PTS2 but not PTS1 import. Taken together, these data provide an explanation for the different protein import defects in CG2 patients and show that the long isoform of the Pex5 protein is required for peroxisomal import of PTS2 proteins.
Analysis of experimental bone tools from Swartkrans Cave, South Africa

Early Pleistocene deposits from Swartkrans Cave, South Africa, yield the remains of Paranthropus robustus and ungulate bone fragments that were manipulated through short-term use. An experimental tool set (n=30) modeled after those from Swartkrans Cave was created using fresh ungulate long bones to demonstrate wear caused by extracting termites, tubers, or both resources, and molded after 30, 60, 90 and 120 minutes of use. Scratch length, breadth, and angle were recorded for all scratches < 80 μm in breadth. The highest standard deviation of scratch angle is seen in the tools used to dig both termites and tubers, whereas the lowest standard deviation is seen in the tools used for digging only termites. Statistical comparison of these results with original bone tool data from Swartkrans suggests that P. robustus, utilized the bone tools for termite harvesting. These results have implications for reconstructing the diet of early hominins in southern Africa. INDEX WORDS: Bone, Tool, Australopithecus, Evolution, Diet, Paleoanthropology, Tuber, Termite, Swartkrans, Hominin, Paranthropus, South Africa ANALYSIS OF EXPERIMENTAL BONE TOOLS FROM SWARTKRANS CAVE, SOUTH AFRICA
Built-in face recognition for smart photo sharing in mobile devices

This paper presents a smart photo sharing application for mobile devices based on an efficient yet powerful face recognition engine. The system allows registering subjects either from live video (mobile camera) or from still images, linking the obtained biometric information to the already existing phone contacts. The photo sharing application allows the user to select images which will be automatically processed with the built-in face recognition module based on Local Binary Patterns: already registered contacts will be identified, so that the current picture can be sent to them in a smart, user-friendly manner. The application also allows to tag unknown subjects and store (or update) their biometric profiles. All the processing is done in the mobile device. The current application runs on Android O.S. , having been tested in two mobile platforms: HTC Desire and Samsung Galaxy Tab. The computational burden for each of the processing modules is provided in both devices, demonstrating the feasibility of the proposed approach for mobile platforms.
Effect of Teacher's Qualification on the Performance of Senior Secondary School Physics Students: Implication on Technology in Nigeria

The study examined the effect of teacher’s qualification on the performance of Senior Secondary School students in Physics. The purpose was to determine whether the status of the teacher has any impact on the performance of the students in Physics. The survey type of descriptive research design was adopted. The sample for the study consisted of 100 Senior Secondary Schools Physics students in Ekiti State and the teachers that prepared and presented the students in each school for 2009/2010 West African School Certificate Examination. The year’s result summary for each school was collated with the bio-data of their respective Physics teachers. Four hypotheses were postulated and tested at 0.05 significance level. The data collated were analysed using inferential statistics. The results revealed that students taught by teachers with higher qualifications performed better than those taught by teachers with lower qualifications. It was also showed that students performed better in physics when taught by professional teachers. The result also showed that teacher’s gender has no effect on their ability to impact knowledge on the students, much as he/she is a skilled teacher in that field of study. However, the experience of the teacher is significant at impacting the students’ academic performance in Physics. Based on the findings, it was recommended that experienced teachers with professional qualifications in higher level should teach Physics at the certificate class.
International Journal of Information Management on the Governance of Information: Introducing a New Concept of Governance to Support the Management of Information

Information governance as an approach to better govern the use of information within and outside an organization is rapidly gaining popularity. A common and scientific ground for this approach has not yet been formulated. In this article the authors describe a definition for information governance, extending the common, one-dimensional approach into a more generic statement. Starting from the well-known principles of IT governance the authors further explore the aspects of both information and governance. Four hypotheses are proposed to give ground to the use of information governance. These hypotheses will be the basis for further research.
Laparoscopic Nissen-Rossetti fundoplication for gastroesophageal reflux disease patients after 2-year follow-up.

INTRODUCTION Gastroesphageal reflux disease (GERD) is a common condition in the general population, affecting patients' quality of life and predisposing to Barrett's esophagus and its most fearsome complication, esophageal adenocarcinoma. The aim of this study is to compare objective and subjective outcomes of laparoscopic Nissen-Rossetti fundoplication after 2 years of follow-up. SUBJECTS AND METHODS Seventy-six GERD patients underwent laparoscopic Nissen-Rossetti fundoplication. Patients were subjected to close follow-up. RESULTS The DeMeester and Johnson score average decreased from a mean preoperative value of 35.48 (SD±40.24) to 9.83 (SD±6.40) at 6 months; at 12 months it was 11.44 (SD±10.28), and at 24 months it was 10.25 (SD±5.61). GERD Health-Related Quality of Life decreased from a preoperative value of 23.04 (SD±11.59) to 9.84 (SD±8.98) at 6 months, 8.34 (SD±8.98) at 12 months, and 6.8 (SD±6.46) at 24 months. The Short Form-36 measurement showed significant improvement. CONCLUSIONS GERD patients need adequate reflux control. Successful antireflux surgery is more effective than medical therapy in preventing both acid and bile reflux. Surgical therapy is effective in terms of reflux control and improvement in quality of life. Strict and rigorous follow-up with both subjective and objective tests is important in order to identify asymptomatic recurrence of reflux after surgery.
Cell proliferation and oncogene expression after bile duct ligation in the rat: Evidence of a specific growth effect on bile duct cells

The proliferative response of the rat liver was measured after temporary or permanent total biliary obstruction (BDO) and in different regions after selective ligation of the lobar ducts draining the right 60% of the hepatic mass. The results were compared with those after 70% partial hepatectomy (PH). Cell proliferation was assessed globally by measuring DNA synthesis and stratified to the separate cell populations with cytostaining techniques that allowed distinction of hepatocytes, duct cells, and nonparenchymal cells (NPCs). In selected experimental groups, gene expression was determined of transforming growth factor‐β1 (TGFβ‐1), prothrombin, c‐erb‐B2, transforming growth factor alpha (TGFα), human Cyclophilin (CyP), and 28S ribosomal RNA. The stimulation of a proliferative response to total BDO required obstruction for longer than 24 hours, but after this deligation did not switch off regeneration. In the first week after permanent BDO, there was progressive infiltration of NPCs, fibrous linkage of some portal areas, and a crescendo of DNA synthesis that was obvious at 24 hours, maximal at 48 hours, and back nearly to baseline at 6 days. At the 2‐day mark, the bile duct cells had a 17‐fold increase in proliferation, accompanied by a threefold to fourfold increase in hepatocyte renewal. Litle or no increase in expression of TGFα or the hepatocyte‐specific prothrombin gene was detectable in the first 48 hours, whereas levels of the oncogene c‐erb‐B2 that is associated with cholangiocarcinoma were expressed from 48 to 96 hours. Livers subjected to regional BDO with or without immunosuppressive treatment with FK 506 and cyclosporine had an inflammatory reaction only on the side with ligated ducts. DNA synthesis increased in both the obstructed and freely draining lobes to approximately half the level that occurred after total BDO. The proliferation of the obstructed side was similar to the mixed duct cell/hepatocyte response after total BDO, but this almost exclusively involved duct cells on the freely draining side. In contrast to the findings after BDO, livers after PH regenerated maximally at 24 hours rather than 48 hours, had a predominantly noninflammatory hepatocyte as opposed to duct cell response, and had marked expression of the prothrombin and TGFα genes but only weakly and late of c‐erb‐B2 messenger RNA. The results show that the liver responds as a whole and in a biologically intelligent way to the nature of the injury inflicted on any part of it. It further implies the presence of humoral communications and control networks that assure organ homeostasis and relate this to total body homeostasis. (HEPATOLOGY 1995; 21:1070–1078.)
Empirical Models for Dark Matter Halos. II. Inner Profile Slopes, Dynamical Profiles, and ρ/σ3

We have recently shown that both the Prugniel-Simien model and Sérsic's function (hereafter referred to as the Einasto model when applied to internal density profiles) describe simulated dark matter halos better than a Navarro-Frenk-White-like model with an equal number of parameters. Here we provide analytical expressions for the logarithmic slopes of these models and compare them with data from real galaxies. Depending on the Einasto parameters of the dark matter halo, one can expect an extrapolated inner (0.01-1 kpc) logarithmic profile slope ranging from approximately -0.2 to approximately -1.5, with a typical value at 0.1 kpc around -0.7. Application of this (better fitting) model therefore alleviates some of the past disagreement with observations on this issue. In addition, we provide useful expressions for the concentration and assorted scale radii: rs, r-2, re, Re, rvir, and rmax, the radius where the circular velocity profile has its maximum value. We also present the circular velocity profiles and the radial behavior of ρ(r)/σ(r)3 for both the Einasto and Prugniel-Simien models, where σ(r) is the velocity dispersion associated with the density profile ρ(r). We find this representation of the phase-space density profile to be well approximated by a power law with a slope slightly shallower than -2 near r = r-2.
Journalistic Responses to Technological Innovation in Newsrooms

This study seeks to investigate how journalists at leading national US newspapers and wire services grapple with the impact of technological changes, especially the introduction and growing use of social media in newsrooms. Using a qualitative methodological approach involving in-depth, semi-structured interviews with journalists employed at leading national and regional news organizations such as The New York Times, The Washington Post, The Wall Street Journal, Los Angeles Times, The Dallas Morning News, Bloomberg News, Reuters and the Associated Press, we explore how journalists view the impact of the growing use of social media, specifically Twitter, on their work environment. We find that while they acknowledged that Twitter facilitated aspects of their work, they almost universally perceived the growing use of this technology as contributing to a variety of tensions and potential conflicts within the newsroom.
Sparse Distributed Memories in a Bounded Metric State Space : Some Theoretical and Empirical Results

Sparse Distributed Memories (SDM) [7] is a linear, local function approximation architecture that can be used to represent cost-to-go or stateaction value functions of reinforcement learning (RL) problems. It offers a possibility to reconcile the convergence guarantees of linear approximators and the potential to scale to higher dimensionality typically exclusive to nonlinear architectures. We investigated both avenues to see if SDM can fulfill its promises in the context of a RL problem with a bounded metric state space. On the theoretical side, we found that using properties of interpolative approximators provided by [3], it can be proven that a version of Q-learning converges with probability one when it is used with a SDM architecture. On the other hand, an important nondivergence result on the SARSA algorithm, an approximate, optimistic policy iteration algorithm, failed to apply in our case because of our loose assumptions on the nature of the state space. However, one of the most important convergence result in reinforcement learning [6], the convergence of TD(λ) was successfully translated into the language of measure theory to cover the case of Markov processes with a general probability state space. This forms the foundation for an eventual proof of convergence of an approximate policy iteration algorithm. On the empirical side, the first step was to design and implement a specialized data structure to store and retrieve “hard locations” (basis points). The specifications of this hash-based data structure will be discussed, as well as statistics on the performances of SDM equipped with this data structure. We conclude by presenting potential extensions to SDM. Their motivations and drawbacks will be examined, focusing on the implications related to the hard location storage data structure. These results form our basic toolbox for our current work targeting a general-purpose, “tweaking-free” reinforcement learning algorithm with flexible assumptions on the space, convergence guarantees and high-dimensional scalability.