Miracle-dz/UniFAR-FTUs huggingface dataset:
Calculation of the Stability of the IS6110 Banding Pattern in Patients with Persistent Mycobacterium tuberculosis Disease

ABSTRACT The interpretation of molecular epidemiologic data of Mycobacterium tuberculosis infection is dependent on the understanding of the stability and evolutionary characteristics of the DNA fingerprinting marker used to classify clinical isolates. This study investigated the stability of the IS6110 banding pattern in serial tuberculosis isolates collected from patients resident in an area with a high incidence of tuberculosis. Evolutionary changes were observed in 4% of the strains, and a half-life (t1/2) of 8.74 years was calculated, assuming a constant rate of change over time. This rate may be composed of a high rate of change seen during the early disease phase (t1/2 = 0.57 years) and a low rate of change seen in the late disease phase (t1/2 = 10.69 years). The early rate probably reflects change occurring during active growth prior to therapy, while the low late rate may reflect change occurring during or after treatment. We demonstrate that the calculation of these rates is strongly influenced by the time interval between onset of disease and sputum sampling. These calculations are further complicated by partial replacement of the original strain population, resulting in the sporadic appearance of clonal variants in sputum specimens. Therefore, the true extent of genetic diversity may be underestimated within each host, thereby influencing molecular epidemiological data used to establish transmission chains.
A Robust, Target-Driven, Cell-Based Assay for Checkpoint Kinase 1 Inhibitors

Checkpoint kinase 1 (Chk1), a serine/threonine kinase, plays an important role in DNA damage checkpoint control and is an attractive target for cancer treatment. To develop a Chk1-specific cell-based assay, stable clones were established in which Chk1 kinase domain fused at its N-terminus with p53 through 4 tandem repeats of Gly-Gly-Gly-Gly-Ser was expressed in an inducible manner. Chk1 kinase specificity of the phosphorylation of fused p53 was confirmed by the experiments with a kinase-inactive Chk1. Only in the presence of an inducer molecule was phosphorylation of p53 at Ser-15 in the stable clones induced. Furthermore, its assay performance proved acceptable for high-throughput screening applications, judging from the Z′ factor values (> 0.77). Finally, the cell-based assay thus established yielded structure-activity relationship data for a small set of test inhibitors of Chk1 within cells. Collectively, these results demonstrate that the established cell-based assay provides a novel and highly sensitive cellular platform for Chk1 inhibitor discovery. (Journal of Biomolecular Screening 2007:809-817)
A DSGE model with endogenous offshoring

I construct a two-country dynamic stochastic general equilibrium (DSGE) model with endogenous offshoring. Firms decide on both the range of offshored activities (extensive margin) and the imported quantities of each intermediate input (intensive margin). The extensive margin is pinned down by a trade-off between a lower wage bill abroad and task-specific offshoring costs in the vein of Grossman and Rossi-Hansberg (2006). Calibrating the model to EMU and CEEC data, I explore the consequences of falling offshoring costs on macroeconomic volatility. I find that lower offshoring costs raise the volatility of output in the high-wage country. For the low-wage country, there is a U-shaped relationship. While the volatility of total employment hardly changes in both countries, real wages become more volatile.
Characterization and Comparison of Na+, K+ and Ca2+ Currents Between Myocytes from Human Atrial Right Appendage and Atrial Septum

Atrial pacing to reduce paroxysmal atrial fibrillation recurrences is performed in right atrial appendage (RAA) traditionally. However, recent studies indicate that atrial septal (AS) pacing produces better outcomes than the RAA pacing. The underlying mechanisms for this difference remained unclear. One possible explanation for the superiority of AS pacing over RAA pacing is that the two different regions have distinct electrophysiological properties. The study was to explore whether there indeed exist regional differences of electrical activities between RAA and AS, using whole-cell patch clamp techniques. The results showed that RAA cells had longer action potential duration, more negative resting potential and greater amplitude of action potential, whereas AS cells had more rapid depolarizing velocity. The sodium current was significantly smaller in RAA cells, whereas the calcium current was markedly smaller in AS cells. The transient outward K+ current was similar in both regions. The ultrarapid delayed rectifier K+ current was greater in RAA than that in AS cells. The inward rectifier K+ current was similar at potentials more negative to -60 mV in both regions. The results indicate that RAA and AS of patients with rheumatic heart disease possess distinct electrophysiological properties. These differences provided a rational explanation for the different efficacies in treating atrial fibrillation by atrial pacing in RAA and AS regions.
Medcenter Container Terminal SpA Uses Simulation in Housekeeping Operations

Within a maritime container terminal, we refer to the operations required to reposition containers in the storage yard as housekeeping. The objective of housekeeping operations, which are typically performed a few hours prior to boarding time, is to accelerate container loading on outgoing vessels. In this paper, we describe our experiences in modeling and simulating the housekeeping process and integrating the related simulation tool into the existing container management system at Medcenter Container Terminal SpA MCT, the company that runs the container terminal at the port of Gioia Tauro, Italy. MCT planners use this operations research tool to perform quantitative analysis of different scenarios to evaluate alternative policies and rules for housekeeping; hence, they can provide more rapid container loading for shipping companies.
Asociación entre la Temperatura Ambiental y Temperatura Superficial del Mar sobre la Aparición de Casos de Ciguatera en el Departamento de San Andrés y Providencia

La ciguatera causa un impacto a la salud y a la economia, producto de su significativa morbilidad, perdida de dias de trabajo, dias de hospitalizacion y en algunos casos la muerte; ademas afecta la economia de los paises caribenos, que en su mayoria dependen de la pesca y del turismo. Cambios inducidos por el clima se han atribuido ser los principales impulsores de la estimulacion, distribucion e intensificacion de dinoflagelados causantes de ciguatera. Este estudio pretende estimar la asociacion entre la temperatura (media, minima absoluta, maxima absoluta, media de minimas, media de maximas y la temperatura superficial del mar media) sobre la aparicion de casos de ciguatera en San Andres y Providencia. Inicialmente se realizo un analisis descriptivo de los casos y brotes notificados al Sistema de Vigilancia en Salud publica compatibles con la definicion de caso establecida en el Protocolo de vigilancia de intoxicaciones por toxinas de algas marinas y se obtuvieron las incidencias para el departamento. Se realizo analisis de varianza y de covarianza (intervalo de confianza del 95%) para identificar asociaciones entre brotes, incidencias y las diferentes temperaturas. Adicionalmente se determino el coeficiente de correlacion de Pearson entre dos series de tiempo (temperaturas Vs. brotes y temperaturas Vs. incidencias) y el intervalo de confianza del 95% con Bootstrap para cada una. Se identificaron 101 casos, 21 brotes y 14 casos aislados. La mayor frecuencia de brotes fue producida por barracuda y jurel. El 53% de los casos pertenecieron al sexo masculino, el grupo de edad mas afectado fue 30 a 44 anos; el periodo de incubacion entre 30 minutos y 24 horas. Hogares y restaurantes fueron los lugares de ocurrencia de los casos. Se establecio una incidencia media anual de 17.4 casos de ciguatera por 100 000 habitantes. En el ANOVA no se identificaron diferencias significativas entre promedios mensuales y anuales de los brotes ni de las incidencias de casos de ciguatera. Para el ANACOVA se encontraron significativas para brotes las temperaturas ambiental maxima absoluta (p = 0.0254) y la ambiental minima absoluta con dos meses de retraso (p = 0.0190). Para incidencias se encontro significativa la temperatura superficial del mar media con dos meses de retraso (p = 0.0387). En el analisis de Bootstrap para brotes se encontro significativa la temperatura ambiental maxima absoluta, la cual muestra una correlacion de 0.335 (IC 95%: 0.063 – 0.560) y en el analisis para incidencias se encontro significativa la temperatura ambiental media de maximas, la cual muestra una correlacion de 0.181 (IC 95%: -0.181 – 0.474). Se recomienda realizar este tipo de analisis con otras variables que puedan influir en la presencia de casos.
Atlantoaxial Subluxation

Twenty-nine patients with atlantoaxial subluxation (18 with rheumatoid arthritis, 2 due to trauma, 4 with os odontoideum, and one each with polyarteritis nodosa, rheumatic fever, Klippel-Feil syndrome, achondroplasia, and cause unknown) were evaluated using a 0.22 tesla resistive MRI unit. Cord compression was classified into four grades according to the degree on magnetic resonance imaging. There were 7 patients with no thecal sac compression (grade 0), 10 with a minimal degree of subarachnoid space compression without cord compression (grade 1), 7 with mild cord compression (grade 2), and 5 with severe cord compression or cord atrophy (grade 3). Although the severity of myelopathy showed poor correlation with the atlantodental interval on conventional radiography, high correlation was observed between MR grading and the degree of myelopathy. The high signal intensity foci were observed in 7 of 12 patients with cord compression (grades 2 and 3) on T2 weighted images. Other frequently observed findings in rheumatoid arthritis included soft tissue masses of low to intermediate signal intensity in the paraodontoid space, erosions of the odontoid processes, and atlantoaxial impaction on T1 and T2 weighted images.
Monetary and Economic Union in West Africa: An Analysis on Trade

Purpose - This paper makes an analysis of trade in the WAMZ as well as the WAMZ's trade with other countries in West Africa, Europe and Asia based on the Optimal Currency Area (OCA) theory. This theory first proposed by Mundell (1961) as a basis for evaluating whether or not an area constitutes an optimal currency area is exploited in assessing whether or not the WAMZ constitutes an OCA. Methodology/Design/Approach - Data utilized for the trend analysis were sourced from the World Bank's World Development in dicator (WDI) and annual reports of the central bank of each WAMZ member country considered. The data spans from 2002 to 2013 and it covers five (5) WAMZ member countries. Similarly, data for the trade analysis was sourced from the World Bank's World Integrated Trade Solution (WITS) and it for the period 2000 to 2012. Findings - While, I found strong evidence against trade symmetry in the WAMZ, there are some evidence of marginal convergence in inflation, real GDP growth and monetary policy rate. Moreover, while I found reasons to believe that the convergence is partially as a result of the convergence criteria, trade in WAMZ remains significantly low and more so for WAMZ's trade in West Africa. Originality/value - This paper concludes that on the basis of trade, WAMZ does not qualify as an OCA. This means that more time is needed for convergence of intra WAMZ trade and in this regard, this paper supports the WAMI's declaration of achieving integration in the year 2020.
Extraction-Free, Filter-Based Template Preparation for Rapid and Sensitive PCR Detection of Pathogenic Parasitic Protozoa

ABSTRACT Within the last several years, the protozoan parasitesCyclospora cayetanensis, Cryptosporidium parvum, and microsporidia have become recognized as important, rapidly emerging human pathogens in immunocompromised and immunocompetent individuals. Since the early 1990s, many of the reported outbreaks of enteric illness caused by these microorganisms have been attributed to food- and water-borne contamination. Many inherent obstacles affect the success of current surveillance and detection methods used to monitor and control levels of contamination by these pathogens. Unlike methods that incorporate preenrichment for easier and unambiguous identification of bacterial pathogens, similar methods for the detection of parasitic protozoa either are not currently available or cannot be performed in a timely manner. We have developed an extraction-free, filter-based protocol to prepare DNA templates for use in PCR to identify C. cayetanensis andC. parvum oocysts and microsporidia spores. This method requires only minimal preparation to partially purify and concentrate isolates prior to filter application. DNA template preparation is rapid, efficient, and reproducible. As few as 3 to 10 parasites could be detected by PCR from direct application to the filters. In studies, as few 10 to 50 Encephalitozoon intestinalis spores could be detected when seeded in a 100-μl stool sample and 10 to 30C. cayetanensis oocysts could be detected per 100 g of fresh raspberries. This protocol can easily be adapted to detect parasites from a wide variety of food, clinical, and environmental samples and can be used in multiplex PCR applications.
Interassay and interobserver variability in the detection of anti-neutrophil cytoplasmic antibodies in patients with ulcerative colitis.

Inflammatory bowel disease (IBD) represents a spectrum of disorders that affect the gastrointestinal tract (1). IBD includes two major entities, Crohn disease and ulcerative colitis (UC). Although the etiology of IBD is unknown at present, it is believed to be an immunologically mediated disease (2). Over the last 40 years, various (auto)antibodies have been described in IBD (3). Anti- Saccharomyces cerevisiae antibodies (4) and perinuclear anti-neutrophil cytoplasmic antibodies (pANCAs) (5) have relatively high prevalence in patients with Crohn disease and UC, respectively. Unlike ANCAs present in vasculitis (6) and in Wegener granulomatosis (7), the exact target antigen of UC-associated pANCAs has not been identified (5)(8). As a consequence, immunofluorescence microscopy is the only widely available technique for screening for these antibodies. Commercially available substrates, however, are not standardized, and part of the discrepancy in results could be attributable to differences among the substrates/assays used, as reported recently (9). Moreover, because specific microscopic criteria to distinguish UC-associated pANCAs from pANCAs seen in vasculitis vary among laboratories, discrepant results could also be attributable to an investigator’s interpretation of the fluorescence pattern. Despite these methodologic problems, it has been suggested that the determination of pANCAs in UC could serve as an adjunct to conventional tools in the diagnosis of IBD and could be used for better phenotypic classification of the disease. Therefore, pANCA analysis is widely performed in the context of laboratory evaluation of IBD. The aim of this study was to assess the interassay and interobserver variability in the detection of UC-associated ANCAs. Sera obtained from 50 patients with UC (23 females and 27 males; mean age, 40.7 years; range, 19–75 years), defined according to the Lennard-Jones criteria (10), were studied. The clinical data for this study population are shown in Table 1 of the Data Supplement that accompanies …
Three sides of the same coin: measuring global cognitive impairment with the MMSE, ADAS‐cog and CAMCOG

The total scores of the ADAS‐cog, MMSE and CAMCOG, comprising various cognitive tasks, are widely used to measure a dimension of global cognitive impairment. It is unknown, however, whether this dimension is common to these instruments. This hampers comparisons when either of these instruments is used. The extent to which these instruments share a common dimension of global cognitive impairment and how their scores relate was examined.
Early application of haemostatic powder added to standard management for oesophagogastric variceal bleeding: a randomised trial

Background Acute variceal bleeding (AVB) requires early therapeutic management by experienced endoscopists that often poses logistical challenges for hospitals. We assessed a different management concept with early application of haemostatic powder—which does not require high endoscopic expertise—added to conventional management in a randomised trial. Methods Cirrhotic patients with AVB received standard medical therapy and were randomised to either immediate endoscopy with haemostatic powder application within 2 hours of admission, followed by early elective endoscopy on the next day, that is, within 12–24 hours of admission for definitive treatment (study group) or to early elective endoscopy only (control group). In both groups, failures to achieve clinical haemostasis until the time of early elective endoscopy underwent rescue endoscopy with attempted conventional haemostasis. Primary outcome was endoscopic haemostasis at the elective endoscopy. Results Of 86 randomised patients with AVB, 5/43 in the study group required rescue endoscopy for failure of controlling spurting bleeding (n=4) after powder application or for early bleeding recurrence in one patient who died before repeating rescue endoscopy. In the control group, 13/43 patients required rescue endoscopic haemostasis for failure of clinical haemostasis (12%vs30%, p=0.034). In the remaining patients, early elective endoscopic haemostasis was achieved in all 38 patients in the study group, while all remaining 30 patients in the control group had fresh gastric blood or (10%) spurting bleeding at early elective endoscopy with successful haemostasis in all of them. Six-week survival was significantly improved in the study group (7%vs30%, p=0.006). Conclusion The new concept of immediate powder application improves early clinical and endoscopic haemostasis. This simplified endoscopic approach may have an impact on early and 6-week survival. Trial registration number NCT03061604.
Does a regular exercise program for ankylosing spondylitis influence body image?

Objective: To investigate whether participation in a regular exercise programme by patients with ankylosing spondylitis (AS) had a positive impact on their body image. Methods: Semi-structured interview and several questionnaires assessed exercise compliance, mood and other facets of disease impact. Body image was assessed using the Arthritis Body Experience Scale, which measured the concepts of body totality and body self-consciousness. Results: No correlation was found between exercise for AS and body image. However, body totality correlated with acceptance of illness ( „ = 0.37, p < 0.05) and both measures of body image inversely correlated with depression (p < 0.05). Conclusion: Normally, regular exercise has a positive effect on body image, but in AS, from this small study it seems that the recommended exercise program does not influence body image, which in these patients seems more closely related to mood. This warrants further evaluation, as a better understanding of influences on body image might improve compliance with therapeutic regimens.
Analyzing Offensive Player- and Team Performance in Soccer Using Position Data

As Cruyff said: “You should always ensure that you score one goal more than the opponent. ”. The number of goals, however, does not always reflect the relationships between the teams on the field. In addition, scoring a goal is a rare occurrence. Therefore, coaches are looking for other techniques to measure the offensive playerand team-performance, and so does the KNVB. Link‘s dangerousity is a good method for measuring this, according to the KNVB‘s analyst expert. Therefore, this study has two purposes: (1) to investigate the offensive playerand team-performance of the Dutch national soccer team and (2) to validate Link‘s dangerousity method. This has been done by transforming the data according to Link‘s dangerousity method using a step-by-step Python pipeline. The position data is linked to the event data (e.g., shots, goals) to determine the outcome of an attack. The aggregated features per attack are used for subgroup discovery to find interesting patterns in the data in relation to the outcome of an attack. On the basis of the results of this research, it can be concluded that Link‘s dangerousity is a valid method for measuring playerand team-performance. However, we have investigated that the maximum dangerousity score without the Density feature performs even better.
Dynamic Detection of Communities and Their Evolutions in Temporal Social Networks

In this paper, we propose a novel community detection model, which explores the dynamic community evolutions in temporal social networks by modeling temporal affiliation strength between users and communities. Instead of transforming dynamic networks into static networks, our model utilizes normal distribution to estimate the change of affiliation strength more concisely and comprehensively. Extensive quantitative and qualitative evaluation on large social network datasets shows that our model achieves improvements in terms of prediction accuracy and reveals distinctive insight about evolutions of temporal social networks.
Declared and actual policy of the Russian Central Bank in 2000–2008: how large is the difference? (in Russian)

There is an opinion that the Russian Central Bank's actual policy in 2000–2008 was real exchange rate targeting. At the same time, the Central Bank regularly declared inflation targets, but regularly missed them. We estimate a simple structural threshold VAR model of the Russian economy to test for these two regimes of the CB's policy. Our testing procedure is based on applying the bootstrap to the estimated TVAR model. We find significant nonlinearity (two policy regimes) caused by endogenous switching between regimes based on past month inflation. The Central Bank by changing its targets was not able to commit to inflation reduction in that period of time, hence facing the issue of credible monetary policy. After the global financial crisis the CB declared its commitment to inflation targeting. But, based on our findings, the policy will be successful only if the Central Bank actually commits itself to reaching inflationary goals.
Autobiographical memory characteristics in depression vulnerability: Formerly depressed individuals recall less vivid positive memories

The differential activation hypothesis (DAH; Teasdale, 1988) proposes that individuals who are vulnerable to depression can be distinguished from non-vulnerable individuals by the degree to which negative thoughts and maladaptive cognitive processes are activated during sad mood. While retrieval of negative autobiographical memories is noted as one such process, the model does not articulate a role for deficits in recalling positive memories. Two studies were conducted to compare the autobiographical memory characteristics of never-depressed and formerly depressed individuals following a sad mood induction. In Study 1, features of negative memories of never-depressed and formerly depressed individuals did not differ, either in neutral or sad mood. For positive memories, groups did not differ in neutral mood, but following a sad mood induction, formerly depressed individuals rated their positive memories as less vivid than their never-depressed counterparts. Study 2 examined positive autobiographical memory features more comprehensively and replicated the finding that in a sad mood formerly depressed individuals recalled less vivid positive memories than never-depressed controls. These findings suggest that the phenomenological features of positive memories could represent an important factor in depressive vulnerability, and, more broadly, that depression may be associated with a deficit in the processing of positive material.