Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations in Complement Factor H Impair Alternative Pathway Regulation on Mouse Glomerular Endothelial Cells in Vitro*

Complement factor H (FH) inhibits complement activation and interacts with glomerular endothelium via its complement control protein domains 19 and 20, which also recognize heparan sulfate (HS). Abnormalities in FH are associated with the renal diseases atypical hemolytic uremic syndrome and dense deposit disease and the ocular disease age-related macular degeneration. Although FH systemically controls complement activation, clinical phenotypes selectively manifest in kidneys and eyes, suggesting the presence of tissue-specific determinants of disease development. Recent results imply the importance of tissue-specifically expressed, sulfated glycosaminoglycans (GAGs), like HS, in determining FH binding to and activity on host tissues. Therefore, we investigated which GAGs mediate human FH and recombinant human FH complement control proteins domains 19 and 20 (FH19–20) binding to mouse glomerular endothelial cells (mGEnCs) in ELISA. Furthermore, we evaluated the functional defects of FH19–20 mutants during complement activation by measuring C3b deposition on mGEnCs using flow cytometry. FH and FH19–20 bound dose-dependently to mGEnCs and TNF-α treatment increased binding of both proteins, whereas heparinase digestion and competition with heparin/HS inhibited binding. Furthermore, 2-O-, and 6-O-, but not N-desulfation of heparin, significantly increased the inhibitory effect on FH19–20 binding to mGEnCs. Compared with wild type FH19–20, atypical hemolytic uremic syndrome-associated mutants were less able to compete with FH in normal human serum during complement activation on mGEnCs, confirming their potential glomerular pathogenicity. In conclusion, our study shows that FH and FH19–20 binding to glomerular endothelial cells is differentially mediated by HS but not other GAGs. Furthermore, we describe a novel, patient serum-independent competition assay for pathogenicity screening of FH19–20 mutants.
Determination of organic acids during the fermentation and cold storage of yogurt.

The objective of the present study was the separation and quantification of orotic, citric, pyruvic, lactic, uric, formic, acetic, propionic, butyric, and hippuric acids in a single isocratic analysis by HPLC. Two methods of extraction were compared: 1) acetonitrile and water and 2) . 01N H2SO4. Recoveries of orotic, lactic, acetic, and propionic acids were 90% for both methods. Recoveries of citric, pyruvic, uric, butyric, and hippuric acids were not satisfactory with the acetonitrile method, but were acceptable using the H2SO4 extraction procedure. Yogurts were manufactured under laboratory-scale conditions, and samples were analyzed during fermentation and after storage at 4 degrees C. Samples were analyzed for pH and organic acids. All of the organic acids exhibited varying degrees of increases and decreases during fermentation and storage. Formic and butyric acids were not detected under the conditions of this study.
Efficacy and tolerability of tegaserod in constipation dominant irritable bowel syndrome.

OBJECTIVE To determine the efficacy and tolerability of tegaserod in the treatment of symptoms of irritable bowel syndrome (IBS) IBS-C patients. DESIGN An open label (quasi interventional) study. PLACE AND DURATION OF STUDY Patients were enrolled between October 2000 and August 2001 at 4 centres (AKUH, Karachi; Mayo Hospital, Lahore; PIMS, Islamabad; Hayatabad Teaching Complex, Peshawar). PATIENTS AND METHODS Tegaserod was administered in a dose of 6 mg (twice-a-day) orally for a period of 6 weeks. Symptoms were assessed before and during treatment using a questionnaire. RESULTS The mean age of patients was 37.5 years and 81(69.2%) were males. The study enrolled 117 patients and 101 patients completed the study. Number of bowel movements, symptoms of straining at defecation, stool consistency, bloating, urgency and abdominal pain improved significantly following treatment (p<0.05). Analysis of data in both genders separately showed statistically significant improvement in symptoms of urgency, straining at defecation, abdominal pain and number of bowel movements following treatment. Side effects of diarrhoea and vertigo (6 and 1 patients respectively) necessitating discontinuation of treatment were infrequent. CONCLUSION Tegaserod given in a dose of 6 mg b.d. is effective and well tolerated in IBS-C patients. It is equally effective in males and females in relieving the symptoms of abdominal pain, bloating, straining at defecation as well as increased in the mean number of bowel movements per week.
Lipid Rafts and Caveolae as Portals for Endocytosis: New Insights and Common Mechanisms

Clathrin‐coated pits and caveolae are two of the most recognizable features of the plasma membrane of mammalian cells. While our understanding of the machinery regulating and driving clathrin‐coated pit‐mediated endocytosis has progressed dramatically, including the elucidation of the structure of individual components and partial in vitro reconstitution, the role of caveolae as alternative endocytic carriers still remains elusive 50 years after their discovery. However, recent work has started to provide new insights into endocytosis by caveolae and into apparently related pathways involving lipid raft domains. These pathways, distinguished by their exquisite sensitivity to cholesterol‐sequestering agents, can involve caveolae but also exist in cells devoid of caveolins and caveolae. This review examines the current evidence for the involvement of rafts and caveolae in endocytosis and the molecular players involved in their regulation.
Kidney injury molecule‐1 in renal disease

Kidney injury molecule‐1 (KIM‐1) is a marker for renal proximal tubular damage, the hallmark of virtually all proteinuric, toxic and ischaemic kidney diseases. KIM‐1 has gained increasing interest because of its possible pathophysiological role in modulating tubular damage and repair. In this respect, it is interesting that the best biomarkers often turn out to be important in modulation of damage and some even become therapeutic targets. The emphasis of this review is on structural and biochemical aspects of KIM‐1, its expression pattern and its pathophysiological role in renal disease. We also discuss the prognostic impact of KIM‐1 in relation to urinary protein excretion. Glomerular (proteinuria) and interstitial markers (KIM‐1) might have independent prognostic impact and so may provide independent treatment targets. Finally, the potential of KIM‐1 as biomarker of renal damage, as a predictor of renal function decline and its perspectives for monitoring therapy response, are discussed. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Impact of surgical staging in women with locally advanced cervical cancer.

OBJECTIVE The aim of this study was to evaluate the impact of surgical staging in the treatment and outcome of women with locally advanced cervical cancer. METHODS Ninety-eight women with locally advanced cervical cancer treated between 1993 and 1997 were retrospectively reviewed. Survival probabilities were calculated by the Kaplan-Meier product limit method and compared with the log-rank test. RESULTS Of the 98 women treated over the 5-year period, 86 were surgically staged: 61 by a retroperitoneal approach, 18 by laparoscopy, and 7 by laparotomy. Median blood loss was 120 cc and median length of hospitalization was 3 days. Preoperative CT scans (n = 55), when compared with surgical findings, missed macroscopic nodal disease in 20% and microscopic disease in 15% and overcalled disease in 10% of cases. Lymph node metastases were found in 45/86 patients (52%): 12 microscopic and 33 macroscopic. The highest level of nodes found to be involved was pelvic in 23, common iliac nodes in 3, para-aortic nodes in 14, and scalene nodes in 5 cases. Of the 86 patients, 49 received pelvic radiation, 27 received extended field radiation, and 10 were identified for palliative treatment only (5 scalene node metastasis, 5 extensive intraperitoneal disease). For node-negative patients, 5-year survival was 74%; for microscopic nodal involvement it was 58%; and for macroscopic involvement it was 39% (P = 0.007). Five-year survival for women with para-aortic node involvement was 52%. Number of nodes involved was a significant prognostic variable (P = 0.008). Patients who received chemotherapy had a 5-year survival of 68% compared to 35% for those who did not (P = 0.06). Factors which did not affect survival included age, histology, type of surgery, stage, and type of radiation (pelvic vs extended). CONCLUSION Surgical staging of women with locally advanced cervical cancer can be performed with acceptable morbidity and it provided more accurate information than CT scans and resulted in a modification of the standard pelvic radiation field for 43% of our patients. The information obtained from surgical staging allows better individualization of therapy, which may improve overall clinical outcome.
The role of antiphospholipid autoantibodies in the cognitive deficits of patients with systemic lupus erythematosus

Objective: To analyze the role of the antiphospholipid autoantibodies (aPL) on the neuropsychological deficits in systemic lupus erythematosus (SLE) patients, comparing groups of patients with antiphospholipid syndrome (APS; n = 15), SLE with aPL (n = 12), and SLE without aPL (n = 27), and a healthy control group (n = 31). Methods: Patients fulfilled the American College of Rheumatology SLE classification criteria or the Sydney criteria for APS. All participants were woman, and groups were matched on age and education. A standardized cognitive examination classified patients as cognitively declined or impaired according to the American College of Rheumatology. Results: Differences between the groups were found in all of the studied variables, comprising attention and executive functions (sustained and selective attention, fluency, and inhibition), and memory (verbal and visual). Post-hoc analyses showed cognitive performance was equivalent between APS and SLE with aPL. Differences between SLE without aPL and control groups were found only in four of the 10 studied variables, while differences in all but two memory variables were found between SLE without aPL and control groups. Furthermore, cognitive deficit was three times more frequent in APS and SLE with aPL patients than for the control group (80%, 75%, and 16%, respectively), and two times more frequent compared to SLE patients without aPL (48%). Conclusions: Our results support the relationship between aPL and cognitive symptoms in SLE. Also, almost half of the patients with SLE and no aPL showed cognitive problems, pointing to the multifactorial causes of cognitive problems in SLE. Future research with larger sample size is guaranteed to replicate our results.
Antibody-Targeted NY-ESO-1 to Mannose Receptor or DEC-205 In Vitro Elicits Dual Human CD8+ and CD4+ T Cell Responses with Broad Antigen Specificity

Immunization of cancer patients with vaccines containing full-length tumor Ags aims to elicit specific Abs and both CD4+ and CD8+ T cells. Vaccination with protein Ags, however, often elicits only CD4+ T cell responses without inducing Ag-specific CD8+ T cells, as exogenous protein is primarily presented to CD4+ T cells. Recent data revealed that Ab-mediated targeting of protein Ags to cell surface receptors on dendritic cells could enhance the induction of both CD4+ and CD8+ T cells. We investigated in this study if these observations were applicable to NY-ESO-1, a cancer-testis Ag widely used in clinical cancer vaccine trials. We generated two novel targeting proteins consisting of the full-length NY-ESO-1 fused to the C terminus of two human mAbs against the human mannose receptor and DEC-205, both internalizing molecules expressed on APC. These targeting proteins were evaluated for their ability to activate NY-ESO-1–specific human CD4+ and CD8+ T cells in vitro. Both targeted NY-ESO-1 proteins rapidly bound to their respective targets on APC. Whereas nontargeted and Ab-targeted NY-ESO-1 proteins similarly activated CD4+ T cells, cross-presentation to CD8+ T cells was only efficiently induced by targeted NY-ESO-1. In addition, both mannose receptor and DEC-205 targeting elicited specific CD4+ and CD8+ T cells from PBLs of cancer patients. Receptor-specific delivery of NY-ESO-1 to APC appears to be a promising vaccination strategy to efficiently generate integrated and broad Ag-specific immune responses against NY-ESO-1 in cancer patients.
Antibody-Mediated Protection against Mucosal Simian-Human Immunodeficiency Virus Challenge of Macaques Immunized with Alphavirus Replicon Particles and Boosted with Trimeric Envelope Glycoprotein in MF59 Adjuvant

ABSTRACT We have previously shown that rhesus macaques were partially protected against high-dose intravenous challenge with simian-human immunodeficiency virus SHIVSF162P4 following sequential immunization with alphavirus replicon particles (VRP) of a chimeric recombinant VEE/SIN alphavirus (derived from Venezuelan equine encephalitis virus [VEE] and the Sindbis virus [SIN]) encoding human immunodeficiency virus type 1 HIV-1SF162 gp140ΔV2 envelope (Env) and trimeric Env protein in MF59 adjuvant (R. Xu, I. K. Srivastava, C. E. Greer, I. Zarkikh, Z. Kraft, L. Kuller, J. M. Polo, S. W. Barnett, and L. Stamatatos, AIDS Res. Hum. Retroviruses 22:1022-1030, 2006). The protection did not require T-cell immune responses directed toward simian immunodeficiency virus (SIV) Gag. We extend those findings here to demonstrate antibody-mediated protection against mucosal challenge in macaques using prime-boost regimens incorporating both intramuscular and mucosal routes of delivery. The macaques in the vaccination groups were primed with VRP and then boosted with Env protein in MF59 adjuvant, or they were given VRP intramuscular immunizations alone and then challenged with SHIVSF162P4 (intrarectal challenge). The results demonstrated that these vaccines were able to effectively protect the macaques to different degrees against subsequent mucosal SHIV challenge, but most noteworthy, all macaques that received the intramuscular VRP prime plus Env protein boost were completely protected. A statistically significant association was observed between the titer of virus neutralizing and binding antibodies as well as the avidity of anti-Env antibodies measured prechallenge and protection from infection. These results highlight the merit of the alphavirus replicon vector prime plus Env protein boost vaccine approach for the induction of protective antibody responses and are of particular relevance to advancing our understanding of the potential correlates of immune protection against HIV infection at a relevant mucosal portal of entry.
Contribution of Accelerated Degradation to Feedback Regulation of 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase and Cholesterol Metabolism in the Liver*

Accumulation of sterols in endoplasmic reticulum membranes stimulates the ubiquitination of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), which catalyzes a rate-limiting step in synthesis of cholesterol. This ubiquitination marks HMGCR for proteasome-mediated degradation and constitutes one of several mechanisms for feedback control of cholesterol synthesis. Mechanisms for sterol-accelerated ubiquitination and degradation of HMGCR have been elucidated through the study of cultured mammalian cells. However, the extent to which these reactions modulate HMGCR and contribute to control of cholesterol metabolism in whole animals is unknown. Here, we examine transgenic mice expressing in the liver the membrane domain of HMGCR (HMGCR (TM1–8)), a region necessary and sufficient for sterol-accelerated degradation, and knock-in mice in which endogenous HMGCR harbors mutations that prevent sterol-induced ubiquitination. Characterization of transgenic mice revealed that HMGCR (TM1–8) is appropriately regulated in the liver of mice fed a high cholesterol diet or chow diet supplemented with the HMGCR inhibitor lovastatin. Ubiquitination-resistant HMGCR protein accumulates in the liver and other tissues disproportionately to its mRNA, indicating that sterol-accelerated degradation significantly contributes to feedback regulation of HMGCR in vivo. Results of these studies demonstrate that HMGCR is subjected to sterol-accelerated degradation in the liver through mechanisms similar to those established in cultured cells. Moreover, these studies designate sterol-accelerated degradation of HMGCR as a potential therapeutic target for prevention of atherosclerosis and associated cardiovascular disease.
Effects of Social Interaction Dynamics on Platforms

Abstract Despite the increasing relevance of online social interactions on platforms, there is still little research on the temporal interaction dynamics between electronic word-of-mouth (eWOM, a form of opinion-based social interaction), popularity information (a form of action-based social interaction), and consumer decision making. Drawing on a panel data set of more than 23,300 crowdfunding campaigns from Indiegogo, we investigate the dynamic effects of these social interactions on consumers’ funding decisions using the panel vector autoregressive methodology. Our analysis shows that both eWOM and popularity information are critical influencing mechanisms in crowdfunding. However, our overarching finding is that eWOM surrounding crowdfunding campaigns on Indiegogo or Facebook has a significant yet substantially weaker predictive power than popularity information. We also find that whereas popularity information has a more immediate effect on consumers’ funding behavior, its effectiveness decays rather quickly, while the impact of eWOM recedes more slowly. This study contributes to the extant literature by (1) providing a more nuanced understanding of the dynamic effects of opinion-based and action-based social interactions, (2) unraveling both within-platform and cross-platform dynamics, and (3) showing that social interactions are perceived as quality indicators on crowdfunding platforms that help consumers reduce risks associated with their investment decisions. These results can help platform providers and complementors to stimulate contribution behavior and increase the prosperity of a platform.
Evaluation of creatine transport using Caco-2 monolayers as an in vitro model for intestinal absorption.

Creatine is a nutraceutical that has gained popularity in both well-trained and casual athletes for its performance-enhancing or ergogenic properties. The major disadvantages of creatine monohydrate formulations are poor solubility and oral bioavailability. In the present study, creatine transport was examined using Caco-2 monolayers as an in vitro model for intestinal absorption. Confluent monolayers of Caco-2 cells (passage 25-35) were used for the permeability studies. Monolayers were placed in side-by-side diffusion chambers. (14)C-Creatine (0.1-0.5 microCi/mL) was added to either the apical or basolateral side, and the transport of the creatine across the Caco-2 monolayer was measured over a 90-min period. The apical to basolateral transport of (14)C-creatine was small, ranging from 0.2-3% of the original amount appearing on the receiver side in a 90-min period. Interestingly, the basolateral to apical permeability of radiolabeled creatine was substantially greater than that observed in the apical to basolateral direction. Studies with drug efflux transport inhibitors indicate that neither the P-glycoprotein nor multidrug resistance-associated protein is involved in the enhanced basolateral to apical transport of creatine.
Well-Tuned ILS for Extended Team Orienteering Problem with Time Windows

The Team Orienteering Problem with Time Windows (TOPTW) is the extension of the Team Orienteering Problem (TOP) by incorporating the time window constraints. Given a set of nodes including their scores, service times and time windows, the goal is to maximize the total of scores collected by a fixed number of routes considering a predefined time window during which the service has to start. In this paper, we propose a mathematical model for the TOPTW that incorporates more real-world constraints, such as different total travel time \ budgets, different start and end nodes for routes. This extension is motivated by a real-world application, namely the Tourist Trip Design Problem (TTDP). We then propose an Iterated Local Search (ILS) algorithm to solve both TOPTW and TTDP. While there have been multiple research works on ILS for TOP and variants, the challenge remains in determining appropriate parameter values to solve them. Here we apply Design of Experiments (DOE), namely factorial experiment design, to first screen and rank all the parameters thereby allowing us to focus on the parameter search space of the important parameters. We demonstrate that well-tuned ILS leads to improvements in terms of the quality of the solutions. More precisely, it is able to improve 31 best known solution values on benchmark TOPTW instances. Our proposed algorithm is also effective for solving real-world problem instances of the TTDP within a few seconds on a regular desktop machine.
Generalized approximating splitting iterations for solving linear least squares problems in finite dimensions

In this paper, a new special class of splitting iterations for solving linear least squares problems in finite dimensions is defined and their main properties of strong global convergence to any problem solution are derived. The investigation results prove the new splitting iterations to be a generalization of the approximating splitting iterations for solving linear least squares problems in finite dimensions, suggesting their suitability for the robust approximate solution of such problems.
Mitochondrial DNA D-loop sequence variation among 5 maternal lines of the Zemaitukai horse breed

Genetic variation in Zemaitukai horses was investigated using mitochondrial DNA (mtDNA) sequencing. The study was performed on 421 bp of the mitochondrial DNA control region, which is known to be more variable than other sections of the mitochondrial genome. Samples from each of the remaining maternal family lines of Zemaitukai horses and three random samples for other Lithuanian (Lithuanian Heavy Draught, Zemaitukai large type) and ten European horse breeds were sequenced. Five distinct haplotypes were obtained for the five Zemaitukai maternal families supporting the pedigree data. The minimal difference between two different sequence haplotypes was 6 and the maximal 11 nucleotides in Zemaitukai horse breed. A total of 20 nucleotide differences compared to the reference sequence were found in Lithuanian horse breeds. Genetic cluster analysis did not shown any clear pattern of relationship among breeds of different type.
Persistence of the effects of Jet‐A in a microcosm with releases from the sediment

This study investigates both the methods and the multispecies and functional level effects of a release of a complex hydrocarbon mixture from sediments using a 60‐d modified mixed flask culture (MFC) microcosm. Neat Jet‐A was injected and mixed into the sediment with one nondosed and three dosed concentrations. Univariate and multivariate statistical and graphical techniques were used to detect patterns in the data. A slow release of the test material from the spiked sediment layer was obtained, and constituents of Jet‐A were detected. Functional parameters (such as pH) were generally better at determining treatment groups than structural parameters (population densities). Analysis of the ability of the various parameters to detect treatment differences confirms that there is not one best indicator for the status of an ecological structure. Transient but statistically significant outcomes were seen at initial treatment concentrations as low as 2 μl/L. The higher concentration treatment groups could be identified as distinguished from nondosed or lower treatments at the end of the 63‐d experiment. Each of the three multivariate techniques differed in their ability to distinguish treatment groups during the course of the experiment.