Miracle-dz/UniFAR-FTUs huggingface dataset:
An approach for mining service composition patterns from execution logs

A service‐oriented application is composed of multiple Web services to fulfill complex functionality that cannot be provided by individual Web service. The combination of services is not random. In many cases, a set of services are repetitively used together in various applications. We treat such a set of services as a service composition pattern. The quality of the patterns is desirable because of the extensive uses and testing in the large number of applications. Therefore, the service composition patterns record the best practices in designing and developing reliable service‐oriented applications. The execution log tracks the execution of services in a service‐oriented application. To document the service composition patterns, we propose an approach that automatically identifies service composition patterns from various applications using execution logs. We locate a set of associated services using Apriori algorithm and recover the control flows among the services by analyzing the order of service invocation events in the execution logs. We also identify structurally and functionally similar patterns to represent such patterns in a higher level of abstraction regardless of the actual services. A case study shows that our approach can effectively detect service composition patterns. Copyright © 2012 John Wiley & Sons, Ltd.
SALSA – a Sectional Aerosol module for Large Scale Applications

The sectional aerosol module SALSA is introduced. The model has been designed to be implemented in large scale climate models, which require both accuracy and computational efficiency. We have used multiple methods to reduce the computational burden of different aerosol processes to optimize the model performance without losing physical features relevant to problematics of climate importance. The optimizations include limiting the chemical compounds and physical processes available in different size sections of aerosol particles; division of the size distribution into size sections using size sections of variable width depending on the sensitivity of microphysical processing to the particles sizes; the total amount of size sections to describe the size distribution is kept to the minimum; furthermore, only the relevant microphysical processes affecting each size section are calculated. The ability of the module to describe different microphysical processes was evaluated against explicit microphysical models and several microphysical models used in air quality models. The results from the current module show good consistency when compared to more explicit models. Also, the module was used to simulate a new particle formation event typical in highly polluted conditions with comparable results to more explicit model setup.
Disabled‐1 mRNA and protein expression in developing human cortex

Disabled‐1 (Dab1) forms part of the Reelin–Dab1 signalling pathway that controls neuronal positioning during brain development; Dab1 deficiency gives rise to a reeler‐like inversion of cortical layers. To establish a timetable of Dab1 expression in developing human brain, Dab1 mRNA and protein expression were studied in prenatal human cortex. The earliest Dab1 signal was detected at 7 gestational weeks (GW), the stage of transition from preplate to cortical plate, suggesting a role of the Reelin–Dab1 signalling pathway in preplate partition. From 12 to 20 GW, the period of maximum cortical migration, Dab1 expression was prominent in the upper tiers of the cortical plate, to decline after midgestation. Radially orientated apical dendrites of Dab1‐expressing neurons indicated a predominant pyramidal phenotype. Pyramidal cells in hippocampus and entorhinal cortex displayed a more protracted time of Dab1 expression compared to neocortex. In addition, at later stages (18–25 GW), Dab1 was also expressed in large neurons scattered throughout intermediate zone and subplate. From 14 to 22 GW, particularly high levels of Dab1 mRNA and protein were observed in cells of the ventricular/subventricular zone displaying the morphology of radial glia. The partial colocalization of vimentin and Dab1 in cells of the ventricular zone supported a radial glia phenotype. The concentration of Dab1 protein in ventricular endfeet and initial portions of radial processes of ventricular‐zone cells points to a possible involvement of Dab1 in neurogenesis. Furthermore, a subset of Cajal–Retzius cells in the marginal zone colocalized Dab1 and Reelin, and may thus represent a novel target of the Reelin–Dab1 signalling pathway.
On Allocating Goods to Maximize Fairness

We consider the Max-Min Allocation problem: given a set of m agents and a set of n items, where agent A has utility u(A, i) for item i, our goal is to allocate items to agents so as to maximize fairness. Specifically, the utility of an agent is the sum of its utilities for the items it receives, and we seek to maximize the minimum utility of any agent. While this problem has received much attention recently, its approximability has not been well-understood thus far. The best known approximation algorithm achieves a roughly O(\sqrt m}-approximation, and in contrast, the best known hardness of approximation stands at 2. Our main result is an algorithm that achieves a \tilde{O}(n^{\eps})-approximation in time n^{O(1/\eps)} for any \eps=\Omega(log log n/log n). In particular, we obtain a poly-logarithmic approximation in quasi-polynomial time, and for every constant \eps ≫ 0, we obtain an n^{\eps}-approximation in polynomial time. Our algorithm also yields a quasi-polynomial time m^{\eps}-approximation algorithm for any constant \eps ≫ 0. An interesting technical aspect of our algorithm is that we use as a building block a linear program whose integrality gap is \Omega(\sqrt m). We bypass this obstacle by iteratively using the solutions produced by the LP to construct new instances with significantly smaller integrality gaps, eventually obtaining the desired approximation. We also investigate a special case of the problem, where every item has a non-zero utility for at most two agents. This problem is hard to approximate to within any factor better than 2. We give a factor 2-approximation algorithm.
Efficacy of Boesenbergia rotunda Treatment against Thioacetamide-Induced Liver Cirrhosis in a Rat Model

Background. Experimental research in hepatology has focused on developing traditional medicines into potential pharmacological solutions aimed at protecting liver from cirrhosis. Along the same line, this study investigated the effects of ethanol-based extract from a traditional medicine plant Boesenbergia rotunda (BR) on liver cirrhosis. Methodology/Results. The BR extract was tested for toxicity on 3 groups of rats subjected to vehicle (10% Tween 20, 5 mL/kg) and 2g/kg and 5g/kg doses of the extract, respectively. Next, experiments were conducted on a rat model of cirrhosis induced by thioacetamide injection. The rats were divided into five groups and, respectively, administered orally with 10% Tween-20 (5 mL/kg) (normal control group), 10% Tween-20 (5 mL/kg) (cirrhosis control group), 50 mg/kg of silymarin (reference control group), and 250 mg/kg and 500 mg/kg of BR extract (experimental groups) daily for 8 weeks. The rats in normal group were intraperitoneally injected with sterile distilled water (1 mL/kg) 3 times/week, and those in the remaining groups were injected intraperitoneally with thioacetamide (200 mg/kg) thrice weekly. At the end of the 8 weeks, the animals were sacrificed and samples were collected for comprehensive histopathological, coagulation profile and biochemical evaluations. Also, the antioxidant activity of the BR extract was determined and compared with that of silymarin. Data from the acute toxicity tests showed that the extract was safe to use. Histological analysis of the livers of the rats in cirrhosis control group revealed uniform coarse granules on their surfaces, hepatocytic necrosis, and lymphocytes infiltration. But, the surfaces morphologically looked much smoother and the cell damage was much lesser in those livers from the normal control, silymarin and BR-treated groups. In the high-dose BR treatment group, the livers of the rats exhibited nearly normal looking lobular architecture, minimal inflammation, and minimal hepatocyte damage, the levels of the serum biomarkers and liver enzymes read nearly normal, and these results were all comparable to those observed or quantified from the normal and silymarin-treated groups. The BR extract had the antioxidant activity about half of what was recorded for silymarin. Conclusion. The progression of the liver cirrhosis can be intervened using the ethanol-based BR extract, and the liver's status quo of property, structure, and function can be preserved. This capability of the extract warrants further studies exploring the significance of its pharmacologic potential in successfully treating the liver cirrhosis in humans.
Impact of Sex and Menopausal Status on Episodic Memory Circuitry in Early Midlife

Cognitive neuroscience of aging studies traditionally target participants age 65 and older. However, epidemiological surveys show that many women report increased forgetfulness earlier in the aging process, as they transition to menopause. In this population-based fMRI study, we stepped back by over a decade to characterize the changes in memory circuitry that occur in early midlife, as a function of sex and women's reproductive stage. Participants (N = 200; age range, 45–55) performed a verbal encoding task during fMRI scanning. Reproductive histories and serologic evaluations were used to determine menopausal status. Results revealed a pronounced impact of reproductive stage on task-evoked hippocampal responses, despite minimal difference in chronological age. Next, we examined the impact of sex and reproductive stage on functional connectivity across task-related brain regions. Postmenopausal women showed enhanced bilateral hippocampal connectivity relative to premenopausal and perimenopausal women. Across women, lower 17β-estradiol concentrations were related to more pronounced alterations in hippocampal connectivity and poorer performance on a subsequent memory retrieval task, strongly implicating sex steroids in the regulation of this circuitry. Finally, subgroup analyses revealed that high-performing postmenopausal women (relative to low and middle performers) exhibited a pattern of brain activity akin to premenopausal women. Together, these findings underscore the importance of considering reproductive stage, not simply chronological age, to identify neuronal and cognitive changes that unfold in the middle decades of life. In keeping with preclinical studies, these human findings suggest that the decline in ovarian estradiol production during menopause plays a significant role in shaping memory circuitry. SIGNIFICANCE STATEMENT Maintaining intact memory function with age is one of the greatest public health challenges of our time, and women have an increased risk for memory disorders relative to men later in life. We studied adults early in the aging process, as women transition into menopause, to identify neuronal and cognitive changes that unfold in the middle decades of life. Results demonstrate regional and network-level differences in memory encoding-related activity as a function of women's reproductive stage, independent of chronological age. Analyzing data without regard to sex or menopausal status obscured group differences in circuit-level neural strategies associated with successful memory retrieval. These findings suggest that early changes in memory circuitry are evident decades before the age range traditionally targeted by cognitive neuroscience of aging studies.
Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization

ABSTRACT We determined the compositions of bacterioplankton communities in surface waters of coastal California using clone libraries of 16S rRNA genes and fluorescence in situ hybridization (FISH) in order to compare the community structures inferred from these two culture-independent approaches. The compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. Clones from γ-proteobacteria comprised ca. 28% of the libraries, while approximately 55% of the clones came from α-proteobacteria, which dominated the clone libraries. TheCytophaga-Flavobacter group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by FISH differed substantially from the composition implied by the clone libraries. The Cytophaga-Flavobacter group dominated 8 of the 11 communities assayed by FISH, including the two communities assayed using clone libraries. On average only 10% of DAPI (4′,6′-diamidino-2-phenylindole)-stained bacteria were detected by FISH with a probe for α-proteobacteria, but 30% of DAPI-stained bacteria appeared to be in the Cytophaga-Flavobacter group as determined by FISH. α-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while the Cytophaga-Flavobacter group was underrepresented in clone libraries. Our data show that theCytophaga-Flavobacter group can be a numerically dominant component of coastal marine bacterioplankton communities.
Capacity of myeloid and plasmacytoid dendritic cells especially at mature stage to express and secrete HLA‐G molecules

Human leukocyte antigen (HLA‐G), a class Ib major histocompatibility complex molecule, is potentially relevant in the immune response through its various immune cell functions. Its expression noticed in some malignancies has also been shown on macrophages and dendritic cells (DC) in tumoral and inflammatory diseases. As DC constitute a key component in the immune response, this work aimed at assessing the expression of HLA‐G at transcriptional and proteic levels during differentiation and maturation of the different DC subsets. We show that HLA‐G transcription was induced during CD34+‐derived DC differentiation and is associated with a cell‐surface expression in half of cases and with a substantial secretion of soluble HLA‐G in all cases. Results were very similar for monocyte‐derived DC, but there was still a weak HLA‐G cell‐surface expression and a lower level of secretion. On the contrary, HLA‐G transcription was weak in plasmacytoid DC without any HLA‐G cell‐surface expression and with a basal level of secretion. The mechanisms involved in HLA‐G expression appear transcriptional and post‐transcriptional. However, the amount of HLA‐G transcripts and the expression of the protein are not related. HLA‐G expression or secretion by DC may have negative consequences on the function of effective immune cells and also on DC themselves via the interaction with inhibitory receptors expressed by these cells. The capacity of DC to express or secrete HLA‐G should be studied in the context of cellular therapy using DC in addition to its suppressive action in immune response.
A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle

Pathogenic bacteria deliver effector proteins into host cells through the type III secretion apparatus to modulate the host function. We identify a family of proteins, homologous to the type III effector Cif from enteropathogenic Escherichia coli, in pathogens including Yersinia, Photorhabdus, and Burkholderia that contain functional type III secretion systems. Like Cif, this family of proteins is capable of arresting the host cell cycle at G2/M. Structure of one of the family members, Cif homolog in Burkholderia pseudomallei (CHBP), reveals a papain-like fold and a conserved Cys-His-Gln catalytic triad despite the lack of primary sequence identity. For CHBP and Cif, only the putative catalytic Cys is susceptible to covalent modification by E-64, a specific inhibitor of papain-like cysteine proteases. Unlike papain-like enzymes where the S2 site is the major determinant of cleavage-site specificity, CHBP has a characteristic negatively charged pocket occupying surface areas corresponding to the S1/S1′ site in papain-like proteases. The negative charge is provided by a conserved aspartate, and the pocket best fits an arginine, as revealed by molecular docking analysis. Mutation analysis establishes the essential role of the catalytic triad and the negatively charged pocket in inducing cell cycle arrest in host cells. Our results demonstrate that bacterial pathogens have evolved a unique papain-like hydrolytic activity to block the normal host cell cycle progression.
Changes in Dickkopf-1, but Not Sclerostin, in Gingival Crevicular Fluid Are Associated with Peroral Statin Treatment in Patients with Periodontitis

Background and Objectives: Periodontitis is marked by the destruction of alveolar bone. Sclerostin (SOST) and dickkopf-1 (DKK-1) act as inhibitors of the Wingless-type (Wnt) signaling pathway, a key regulator of bone metabolism. Recent studies have suggested that statins play a role in bone resorption and formation by influencing Wnt signaling. The aim of this study was to determine the levels of SOST and DKK-1 in periodontal patients with and without peroral statins treatment in their therapy. Materials and Methods: A total of 79 patients with diagnosed periodontitis were divided into two groups: 39 patients on statin therapy (SP group) and 40 patients without statin therapy as a control group (P group). The periodontal clinical examination probing (pocket) depth (PD) and gingival recession (GR) were measured, and approximal plaque was detected, while vertical and horizontal bone resorption was measured using a panoramic radiograph image. Clinical attachment loss (CAL) values were calculated using PD and GR values. Gingival crevicular fluid (GCF) was collected and used for measuring SOST and DKK-1 levels. A questionnaire was used to assess lifestyle habits and statin intake. Patients’ medical records were used to obtain biochemical parameters. Results: There was no significant difference in sclerostin concentration between the SP and P group. DKK-1 values were significantly higher in the SP group compared to the control group (p = 0.04). Also, PD (p = 0.001) and GR (p = 0.03) were significantly higher in the SP group. The level of DKK-1 had a positive relationship with the PD, the greater the PD, the higher the level of DKK-1 (Rho = 0.350), while there was no significant association with other parameters. Conclusions: Peroral statins in periodontal patients are associated with GCF levels of DKK-1 but not with sclerostin levels.
A Workflow for Meaningful Interpretation of Classification Results from Handheld Ambient Mass Spectrometry Analysis Probes

While untargeted analysis of biological tissues with ambient mass spectrometry analysis probes has been widely reported in the literature, there are currently no guidelines to standardize the workflows for the experimental design, creation, and validation of molecular models that are utilized in these methods to perform class predictions. By drawing parallels with hurdles that are faced in the field of food fraud detection with untargeted mass spectrometry, we provide a stepwise workflow for the creation, refinement, evaluation, and assessment of the robustness of molecular models, aimed at meaningful interpretation of mass spectrometry-based tissue classification results. We propose strategies to obtain a sufficient number of samples for the creation of molecular models and discuss the potential overfitting of data, emphasizing both the need for model validation using an independent cohort of test samples, as well as the use of a fully characterized feature-based approach that verifies the biological relevance of the features that are used to avoid false discoveries. We additionally highlight the need to treat molecular models as “dynamic” and “living” entities and to further refine them as new knowledge concerning disease pathways and classifier feature noise becomes apparent in large(r) population studies. Where appropriate, we have provided a discussion of the challenges that we faced in our development of a 10 s cancer classification method using picosecond infrared laser mass spectrometry (PIRL-MS) to facilitate clinical decision-making at the bedside.
Nutritional Status and Quality of Life of Women with HIV/AIDS

Problem statement: HIV infection is a multisystem disorder which causes chronic infections that lead to profound immune- suppression. Women have always been a vulnerable section of the society. They are doubly vulnerable due to the HIV and malnutrition vicious cycle, which may affect their Quality Of Life (QOL). There are different literature reviews which suggest under-nutrition, wasting due to HIV but it is important to know whether this under-nutrition affects their Quality Of Life (QOL) of these vulnerable women. Approach: This cross sectional study recruited female patients on antiretroviral therapy. Weight, height, grip strength, Tricep Skin Fold (TSF) and Mid Upper Arm Circumference (MUAC) were measured. Nutrient intake was calculated by 24 h recall and food frequency questionnaire. WHO QOL-HIV BREF was used to assess QOL. Results: Among 55 patients, 32 (58.2%), 23 (41.8%) were asymptomatic and symptomatic respectively. The mean adequacies of energy and protein for all the subjects were 57.56 ± 21.89, 61.27 ± 28.50 percent respectively. The Body Mass Index (BMI) of the symptomatic were significantly (p = 0.009) lower than the asymptomatic subjects, the mean being 19.84 ± 3.6 (kg/m2), with 27.3% having BMI < 18.5 (kg/m2). The mean TSF, MUAC, grip strength and hemoglobin level were 10.66 ± 4.36 mm, 23.72 ± 3.43 cm, 16.12 ± 5.03 kg force and 10.8 ± 1.3g/dl respectively. The scores of QOL were correlated positively with all the parameters of nutritional status. Grip strength and hemoglobin level were significantly correlated (p = 0.01) with the scores of four and five domains of QOL respectively. Conclusion: Dietary intake was inadequate, which affected the nutritional status. Conservation of muscle mass and maintenance of hemoglobin levels may improve QOL in HIV infected women. Thus there is a need for nutritional counseling and other nutritional intervention.
Structure and Proposed Activity of a Member of the VapBC Family of Toxin-Antitoxin Systems

In prokaryotes, cognate toxin-antitoxin pairs have long been known, but no three-dimensional structure has been available for any given complex from Mycobacterium tuberculosis. Here we report the crystal structure and activity of a member of the VapBC family of complexes from M. tuberculosis. The toxin VapC-5 is a compact, 150 residues, two domain α/β protein. Bent around the toxin is the VapB-5 antitoxin, a 33-residue α-helix. Assays suggest that the toxin is an Mg-enabled endoribonuclease, inhibited by the antitoxin. The lack of DNase activity is consistent with earlier suggestions that the complex represses its own operon. Furthermore, analysis of the interactions in the binding of the antitoxin to the toxin suggest that exquisite control is required to protect the bacteria cell from toxic VapC-5.