Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid algorithms for subgraph pattern queries in graph databases

Numerous methods have been proposed over the years for subgraph query processing, as it is central to graph analytics. Existing work is fragmented into two major categories. Methods in the filter-then-verify (FTV) category first construct an index of the DB graphs. Given a query, the index is used to filter out graphs that cannot contain the query. On the remaining graphs, a subgraph isomorphism algorithm is applied to verify whether each graph indeed contains the query. A second category of algorithms is mainly concerned with optimizing the Subgraph Isomorphism (SI) testing process (an NP-Complete problem) in order to find all occurrences of the query within each DB graph, also known as the matching problem. The current research trend is to totally dismiss FTV methods, because SI methods have been shown to enjoy much shorter query execution times and because of the alleged high costs of managing the DB graph index in FTV methods. Thus, a number of new SI methods are being proposed annually. In the current work, we initially study the performance of the latest SI algorithms over datasets consisting of a large number of graphs. With our study, we evaluate the algorithms' performance and we provide comparison details with former studies. As a second step, we combine the powerful filtering of a top-performing FTV method, with the various SI methods, which leads to the best practice conclusion that SI and FTV shouldn't be thought of as disjoint types of solutions, as their union achieves better results than any one of them individually. Specifically, we experimentally analyze and quantify the (positive) impact of including the essence of indexed FTV methods within SI methods, showing that query processing times can be significantly improved at modest additional memory costs. We show that these results hold over a variety of well-known SI methods and across several real and synthetic datasets. As such, hybrids of the type reveal a missing opportunity and a blind spot in related literature and trends.
The Substantiation of the Investment Decision

In this paper, we have analysed the mode in which an investment project is substantiated. Starting from the role played by the investments in securing economic growth and macro-stabilization, we granted full attention to conditions and stages to be taken into account in investment design. Of course, an important element in investing are the resources, internal or external, involved in investments. Simultaneously, there must be studied the effect of the economic objectives achieved through investment, especially the modality and recovery of expenses made. For such analysis of investment substantiation, we have followed the design of a model that would be relevant in the impact study. Furthermore, it must be stated that the impact study must be subjected to a procedure of simulation, in the scope of guaranteeing the efficiency of expenses. In the scope of presenting this topic, we have made clear some aspects regarding the investments concept; the classification of investments, the financial contents and elements regarding the investments; the role of investments in the social-economic evolution of a country. In this context, together with the theoretical aspects, we have presented some indicators used in the analysis and substantiation of investment projects.
Uneven distribution of the luxS gene within the genus Campylobacter

Abstract Polymerase chain reaction (PCR) amplification was performed on 20 isolates of five Campylobacter species using a degenerate primer pair designed in silico to generate a product of the luxS gene or its homologue from Campylobacter organisms. Although the primer pair successfully amplified products of approximately 500 base pairs (bp) with the eight isolates of C. jejuni and C. coli and some of C. upsaliensis and C. fetus, it failed to amplify fragments with all four isolates of C. lari (two ureasenegative C. lari; two urease-positive thermophilic campylobacters). When Southern blot hybridisation analysis was carried using the mixed luxS gene fragments prepared from the C. jejuni, C. coli, C. upsaliensis and C. fetus strains as a probe, all C. jejuni, C. coli, C. upsaliensis and C. fetus isolates gave positive signals, but no positive signal was detected with any C. lari isolate. These results clearly indicate that C. jejuni, C. coli, C. upsaliensis and C. fetus carry the luxS gene or its homologue. However, no luxS gene or its homologue was identified to occur in the C. lari genome. Although autoinducer-2 assays were positive in C. jejuni, C. coli, C. upsaliensis and C. fetus isolates, it was negative with all the C. lari isolates examined. In addition, a biofilm formation assay demonstrated that biofilm formation in the C. lari species does not appear to correlate with the occurrence of the luxS gene because biofilm formation occurred among some isolates of C. lari.
Predictive Utility of Brief Alcohol Use Disorders Identification Test (AUDIT) for Human Immunodeficiency Virus Antiretroviral Medication Nonadherence

Alcohol use negatively affects adherence to antiretroviral therapy (ART), thus human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) care providers need accurate, efficient assessments of alcohol use. Using existing data from an efficacy trial of 2 cognitive-behavioral ART adherence interventions, the authors sought to determine if results on 2 common alcohol screening tests (Alcohol Use Disorders Identification Test—Consumption [AUDIT-C] and its binge-related question [AUDIT-3]) predict ART nonadherence. Twenty-seven percent of the sample (n = 308) were positive on the AUDIT-C and 34% were positive on the AUDIT-3. In multivariate analyses, AUDIT-C–positive status predicted ART nonadherence after controlling for race, age, conscientiousness, and self-efficacy (P = .036). Although AUDIT-3–positive status was associated with ART nonadherence in unadjusted analyses, this relationship was not maintained in the final multivariate model. The AUDIT-C shows potential as an indirect screening tool for both at-risk drinking and ART nonadherence, underscoring the relationship between alcohol and chronic disease management.
An insight into the general relationship between the three dimensional structures of enzymes and their electronic wave functions: Implication for the prediction of functional sites of enzymes

In this study, we explored the general relationship between the three‐dimensional (3D) structures of enzymes and their electronic wave functions. Furthermore, we developed a method for the prediction of their functionally important sites. For this purpose, we first performed linear‐scaling molecular orbital calculations for 112 nonredundant, non‐homologous enzymes with known structure and function. In consequence, we showed that the canonical molecular orbitals (MOs) of the enzymes could be classified into three groups according to the degree of electron delocalization: highly localized orbitals (Group A), highly delocalized orbitals whose electrons are distributed over almost the whole molecule (Group B), and moderately delocalized orbitals (Group C). The MOs belonging to Group A are located near the HOMO‐LUMO band gap, and thereby include the frontier orbitals of a given enzyme. We inferred that the MOs of Group B play a role in stabilizing the 3D structure of the enzyme, while those of Group C contribute to constructing the covalent bond framework of the enzyme. Next, we investigated whether the frontier orbitals of enzymes could be used for identifying their potential functional sites. As a result, we found that the frontier orbitals of the 112 enzymes have a high propensity to be colocalized with the known functional sites, especially when the enzymes are hydrated. Such a propensity is shown to be remarkable when Glu or Asp is a functional site residue. On the basis of these results, we finally propose a protocol for the prediction of functional sites of enzymes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Transfusion-associated circulatory overload in orthopedic surgery patients: a multi-institutional study

Abstract Although recognized as a serious complication of hemotherapy, few data are available on the incidence of transfusion-associated circulatory overload (TACO). Detailed demographic and clinical information was obtained from records of 382 Medicare patients undergoing total hip or knee replacements (and receiving transfusions) from January 1992 to December 1993 at five Massachusetts hospitals. Seventy-eight percent of the patients were women with a mean age of 77 years. Thirty-two percent had co-morbidities including myocardial or coronary disease. Transfusion-related complications and comorbidities were identified and reviewed by transfusion experts. Patients were excluded from consideration if non-transfusion factors such as myocardial disease could have contributed to the development of acute pulmonary edema. Four (3 females, 1 male) patients (1.05%) developed TACO postoperatively. Mean age of these patients was 84 years (range, 75–101) versus 77 years for non-TACO. The mean intraoperative estimated blood loss was 375 mL. Each patient received only 1–2 units of red blood cells prior to onset of TACO, and in two cases only autologous blood was used. The mean positive fluid balance was 2,480 mL. The mean pretransfusion hematocrit prior to circulatory overload (CO) was 26.0 percent. symptoms were reversed with diuretics. Length of stay was significantly prolonged by these incidents. TACO is a frequent and serious event in an orthopedic surgical setting. It is associated with advanced age, increased health care costs, and may occur in the setting of modest transfusion volumes. The utilization of conservative transfusion criteria and fluid management in the perioperative setting may decrease the incidence of this complication in this population. Immunohematology 1996;12:87–89.
Bap, a Staphylococcus aureus Surface Protein Involved in Biofilm Formation

ABSTRACT Identification of new genes involved in biofilm formation is needed to understand the molecular basis of strain variation and the pathogenic mechanisms implicated in chronic staphylococcal infections. A biofilm-producing Staphylococcus aureus isolate was used to generate biofilm-negative transposon (Tn917) insertion mutants. Two mutants were found with a significant decrease in attachment to inert surfaces (early adherence), intercellular adhesion, and biofilm formation. The transposon was inserted at the same locus in both mutants. This locus (bap [for biofilm associated protein]) encodes a novel cell wall associated protein of 2,276 amino acids (Bap), which shows global organizational similarities to surface proteins of gram-negative (Pseudomonas aeruginosa andSalmonella enterica serovar Typhi) and gram-positive (Enteroccocus faecalis) microorganisms. Bap's core region represents 52% of the protein and consists of 13 successive nearly identical repeats, each containing 86 amino acids. bap was present in a small fraction of bovine mastitis isolates (5% of the 350S. aureus isolates tested), but it was absent from the 75 clinical human S. aureus isolates analyzed. All staphylococcal isolates harboring bap were highly adherent and strong biofilm producers. In a mouse infection modelbap was involved in pathogenesis, causing a persistent infection.
HIV infection, antiretroviral therapy, and CD4+ cell count distributions in African populations.

BACKGROUND The variability in CD4+ cell counts within and among human immunodeficiency virus (HIV)-positive and -negative African populations has not been explained but has important implications for understanding the incidence of HIV-related opportunistic infections, especially tuberculosis, in both individuals and populations. METHODS In HIV-negative African adults, CD4+ cell counts vary within populations (interquartile ranges [IQRs], 169-603 cells/microL) and among populations (means vary from 699 to 1244 cells/microL), with similarly wide variations in HIV-positive adults. We developed dynamic mathematical models to predict the distribution of CD4+ cell counts in HIV-positive adults using the distribution in HIV-negative adults. RESULTS Under the assumption that survival is independent of the CD4+ cell count before seroconversion, we fitted the observed distributions in HIV-positive adults. At a CD4+ cell count of 200 cells/microL, the median life expectancy of HIV-positive Zambians (4.0 years) was predicted to be 1.7 times that of HIV-positive South Africans (2.3 years). CONCLUSIONS The model provides a way to estimate the changing distribution of CD4+ cell counts and, hence, the changing incidence of HIV-related opportunistic infections as the epidemic matures. This could substantially improve the planning of health services, including the need and demand for antiretroviral therapy. Better data are needed to test the model and its assumptions more rigorously and to fully understand the variability in CD4+ cell counts within and among populations.
T-Cell Subsets That Harbor Human Immunodeficiency Virus (HIV) In Vivo: Implications for HIV Pathogenesis

ABSTRACT Identification of T-cell subsets that are infected in vivo is essential to understanding the pathogenesis of human immunodeficiency virus (HIV) disease; however, this goal has been beset with technical challenges. Here, we used polychromatic flow cytometry to sort multiple T-cell subsets to 99.8% purity, followed by quantitative PCR to quantify HIV gag DNA directly ex vivo. We show that resting memory CD4+ T cells are the predominantly infected cells but that terminally differentiated memory CD4+ T cells contain 10-fold fewer copies of HIV DNA. Memory CD8+ T cells can also be infected upon upregulation of CD4; however, this is infrequent and HIV-specific CD8+ T cells are not infected preferentially. Naïve CD4+ T-cell infection is rare and principally confined to those peripheral T cells that have proliferated. Furthermore, the virus is essentially absent from naïve CD8+ T cells, suggesting that the thymus is not a major source of HIV-infected T cells in the periphery. These data illuminate the underlying mechanisms that distort T-cell homeostasis in HIV infection.
Pemilu Kepala Daerah dalam Transisi Demokrasi

The election of regional head has a strategic position to building democracy in transition. In order that the election of regional head can creating a dignified democracy, the implementation of its should be based on the principle of the general election i.e: independent, fair, equitable, rule of law; the orderly election, transparency, proportionality; professionalism, accountability, efficiency, and effectiveness.
Synthesis of absolutely stabilizing PID controllers and its application to a ball and wheel system

We consider the problem of synthesizing proportional-integral-derivative (PID) controllers that absolutely stabilize a given Lur'e system. Based on the circle criterion and the stability characterization of the strictly positive real property, sufficient conditions for the existence of stabilizing PID controllers are given in terms of simultaneous stabilization of complex polynomials. The results from the earlier work are then used to solve the resulting complex polynomial stabilization problem. For a fixed proportional gain, and by sweeping over a variable, the set of the stabilizing integral and derivative gain values can be determined constructively using linear-programming techniques. The proposed synthesis method is used to design a stabilizing PID controller for the ball and wheel system and the experimental results are also presented.
Development and duration of human papillomavirus lesions, after initial infection.

BACKGROUND To determine the potential value of human papillomavirus (HPV) vaccines, information concerning the incidence and duration of clinically important lesions is needed. METHODS A total of 603 female university students were followed for a mean duration of 38.8 months. Triannual gynecologic examinations included cervical and vulvovaginal specimen collection for Pap and HPV DNA testing. Women with cytologic evidence of a high-grade squamous intraepithelial lesion (SIL) were referred for colposcopically directed biopsy. RESULTS Among women with incident HPV infection, the 36-month cumulative incidence of cervical SILs found by cytologic testing (47.2%; 95% confidence interval [CI], 38.9%-56.4%) was higher than that of vaginal SILs (28.8%; 95% CI, 21.3%-38.2%). The median time to clearance of cervical and vaginal SILs was 5.5 and 4.7 months, respectively. Among women with incident HPV-16 or HPV-18 infection, the 36-month cumulative incidence of cervical intraepithelial neoplasia (CIN) grade 2 was 20.0% (95% CI, 10.8%-35.1%), and that of CIN grade 3 was 6.7% (95% CI, 2.5%-17.0%). The 36-month cumulative incidence of clinically ascertained genital warts among women with incident HPV-6 or HPV-11 infection was 64.2% (95% CI, 50.7%-77.4%). CONCLUSIONS Intraepithelial lesions are common early events among women with incident HPV infection, and the interval between incident HPV-16 or HPV-18 infection and biopsy-confirmed CIN grade 2-3 appears to be relatively short.
Inhibition of cell surface MHC class II expression by Salmonella

Peptide presentation by MHC molecules is an essential component of the adaptive immune response. To persist in a host, many pathogens have evolved strategies that interfere with MHC antigen‐presentation. We show that in human cells harboring intracellular Salmonella, MHC class II cell surface expression was substantially reduced. The effect was specific for MHC class II as expression of additional surface receptors remained unchanged. We investigated the underlying mechanism and showed that class II biosynthesis and peptide loading were unaffected by the presence of Salmonella; however, infection led to an intracellular accumulation of mature molecules. The intracellular class II colocalized with lysosome‐associated membrane protein‐1 and HLA‐DM but not with the Salmonella‐containing vacuole. Using Salmonella mutants defective in different components and effectors of the Salmonella pathogenicity island‐2 type‐III secretion system, we traced the effect on class II to the sifA locus. SifA has been shown to be involved in recruiting membrane for the Salmonella‐containing vacuoles. Our data suggest an additional role for SifA in interfering with MHC class II antigen‐presentation.
Inflammation and the coagulation system in tuberculosis: Tissue Factor leads the dance

Mycobacterium tuberculosis, the causative agent of tuberculosis, drives the formation of granulomas, structures in which both immune cells and the bacterial pathogen cohabit. The most abundant cells in granulomas are macrophages, which contribute as both cells with bactericidal activity and as targets for M. tuberculosis infection and proliferation during the entire course of infection. The mechanisms and factors involved in the regulation and control of macrophage microenvironment‐specific polarization and plasticity are not well understood, as some granulomas are able to control bacteria growth and others fail to do so, permitting bacterial spread. In this issue of the European Journal of Immunology, Venkatasubramanian et al. [Eur. J. Immunol. 2016. 46: 464–479] show that mice lacking the tissue factor gene in myeloid cells have augmented M. tuberculosis growth and increased inflammation in the lungs. This suggests that tissue factor, an initiator of coagulation, is important for the generation of fibrin, which supports granuloma formation. This article demonstrates for the first time the involvement of tissue factor in inducing effective immunity against M. tuberculosis, and sheds new lights on the complex interplay between host inflammatory response, the coagulation system, and the control of M. tuberculosis infection.
Adrenocorticotropin and cortisol response to lysine vasopressin in relation to the outcome of the dexamethasone suppression test in major depressive disorder

ABSTRACT— The pathophysiology behind the abnormalities of the hypothalamic pituitary adrenal cortex axis found in patients with major depressive disorder was studied by the use of the vasopressin test. The response of plasma adrenocorticotropin (ACTH) and cortisol to the injection of 10 IU lysine‐vasopressin (LVP) was investigated in 18 patients meeting the DSM‐III criteria for major depressive episode. The response was correlated to the outcome of the dexamethasone suppression test (DST) with the use of two different cut‐off points, 139 nmol/1 and 200 nmol/1 respectively.
Two colons‐two cancers: Paradigm shift and clinical implications

Embryological and physiological data suggest that proximal (in relation to the splenic flexure) and distal parts of the colon represent distinct anatomical and functional entities. Since 1990, molecular biologists have identified two distinct pathways, microsatellite instability (MSI) and chromosomal instability (CIN), which are involved in the pathogenesis of colon cancer (CC). Thus, a new paradigm has emerged with the discovery that CC is a heterogeneous disease; furthermore recent data have demonstrated that these two distinct pathways in colorectal carcinogenesis are characterized by a different clinical outcome. The implications for the clinicians are twofold; (1) tumors originating from the proximal colon have a better prognosis due to a high percentage of MSI‐positive lesions; and (2) location of the neoplasm in reference to the splenic flexure should be documented before group stratification in ongoing trials of adjuvant chemotherapy for CC. In the future, clinical decision‐making regarding adjuvant chemotherapy might be stratified according to the MSI status of cancers located proximally to the splenic flexure. J. Surg. Oncol. 2004;88:261–266. © 2004 Wiley‐Liss, Inc.
Response to `Comment on “A critical understanding of the fractal model of metabolic scaling'”

The exponent of the scaling of metabolic rate with body mass has been the subject of debate for more than a century. The argument is at two levels, one concerning questions of empirical support for the exponent and the other, how to derive it theoretically. At this second level, the exponent is usually treated as the outcome of an underlying physical burden and approached as the search for a natural law emerging within energetic and geometric constraints. Recently, a model relying on fractal geometry was proposed as a general explanation for the phenomenon. In the present study, a reanalysis of the fractal model is performed to verify its validity. All the conditions that allow for the connection between the geometric proposition and the allometric exponent are evaluated, as well as the energy loss minimization procedure put forward in the model. It is demonstrated that the minimization procedure is mathematically incorrect and ill-posed. Also, it is shown that none of the connecting conditions are fulfilled. Therefore, it is concluded that the fractal model lacks self-consistency and correct statement: it relies on strong assumptions of homogeneity in morpho-physiological features among organisms instead of demonstrating them, as claimed by its authors. It is proposed that empiricists and theoreticians should rather evaluate the frameworks for addressing metabolic scaling phenomena.