Miracle-dz/UniFAR-FTUs huggingface dataset:
A 12-case series of Penicillium marneffei pneumonia.

BACKGROUND Penicillium marneffei, an endemic fungus in Southeast Asia and southern China, is the cause of opportunistic infection in HIV-infected patients who may present with symptoms and signs of the lungs, and abnormal chest radiographs. However, only a few cases of pulmonary infection from this organism have been reported. OBJECTIVE To study the clinical manifestations of patients with Penicillium marneffei pneumonia diagnosed by sputum or bronchoalveolar lavage (BAL) fluid culture MATERIAL AND METHOD Retrospective descriptive study of patients who were diagnosed with Penicillium marneffei pneumonia at Maharaj Nakorn Chiang Mai Hospital from September 1999 to July 2004. RESULTS Twelve patients (eight males, four females) were included with mean age of 36.1 years. Nine cases were HIV-infected. Their presenting symptoms included fever, cough, dyspnea and weight loss. Skin lesions, hepatomegaly and lymphadenopathy were extrapulmonary signs. Chest radiographs revealed diffuse reticulonodular, diffuse reticular, localized alveolar, localized reticular infiltration, and cavitary lesion. The diagnosis was made by cultures from the sputum in five cases and BAL fluid in the others. Co-infections with Streptococcus pneumoniae, Klebsiella pneumoniae, Mycobacterium tuberculosis, Cryptococcus neoformans, and Strongyloides stercoralis were found. Most of them were treated by intravenous amphotericin B followed by oral itraconazole, or oral itraconazole. CONCLUSION Penicillium marneffei pneumonia has non-specific clinical manifestations, it cannot be excluded from other infections and may have co-infections. Physicians should include this infection in their differential diagnosis especially in immunocompromised patients.
CXCL12 Signaling Is Independent of Jak2 and Jak3*

Janus kinases (Jaks) are a small family of cytoplasmic tyrosine kinases, critical for signaling by Type I and II cytokine receptors. The importance of Jaks in signaling by these receptors has been firmly established by analysis of mutant cell lines, the generation of Jak knock-out mice, and the identification of patients with Jak3 mutations. While a number of other ligands that do not bind Type I and II cytokine receptors have also been reported to activate Jaks, the requirement for Jaks in signaling by these receptors is less clear. Chemokines for example, which bind seven transmembrane receptors, have been reported to activate Jaks, and principally through the use of pharmacological inhibitors, it has been argued that Jaks are essential for chemokine signaling. In the present study, we focused on CXCR4, which binds the chemokine CXCL12 or stromal cell-derived factor-1, a chemokine that has been reported to activate Jak2 and Jak3. We found that the lack of Jak3 had no effect on CXCL12 signaling or chemotaxis nor did overexpression of wild-type versions of the kinase. Similarly, overexpression of wild-type or catalytically inactive Jak2 or “knocking-down” Jak2 expression using siRNA also had no effect. We also found that in primary lymphocytes, CXCL12 did not induce appreciable phosphorylation of any of the Jaks compared with cytokines for which these kinases are required. Additionally, little or no Stat (signal transducer and activator of transcription) phosphorylation was detected. Thus, we conclude that in contrast to previous reports, Jaks, especially Jak3, are unlikely to play an essential role in chemokine signaling.
Deletion of the N-terminal region of the AREA protein is correlated with a derepressed phenotype with respect to nitrogen metabolite repression

The entire areA gene and a truncated version lacking the sequence encoding the N-terminal 389 amino acids were expressed from the qutE promoter and terminator in an Aspergillus nidulans strain with the endogenous areA gene deleted. This expression system was used to decouple the effects of transcription regulation and mRNA stability mediated by the native promoter and terminator from any posttranslational modulation of AREA activity. Both the full-length AREA protein and the truncated form were able to function in the deletion strain, conferring the ability to use alternate nitrogen sources. Transformants containing the entire areA gene had a repressible phenotype with respect to nitrogen metabolite repression, whereas those containing the truncated form of the areA gene had a derepressed phenotype. The truncated areA gene was expressed in an A. nidulans strain containing a normally regulated wild-type areA gene, and transformants displayed a quinate-inducible nitrogen metabolite derepressed phenotype. Northern blot analysis of transformed strains showed that areA-specific mRNAs of the expected sizes were being produced. The truncated AREA protein was overproduced in Escherichia coli as a fusion protein and purified to homogeneity by a single-step immobilized metal affinity chromatography, and the purified protein was shown to bind specifically to the niaD promoter. Revised sequences of the 5' region of the areA gene and the entire meaB gene are reported.
Structure of Unsteady Partially Premixed Flames and the Existence of State Relationships

In this study, we examine the structure and existence of state relationships in unsteady partially premixed flames (PPFs) subjected to buoyancy-induced and external perturbations. A detailed numerical model is employed to simulate the steady and unsteady two-dimensional PPFs established using a slot burner under normal and zero-gravity conditions. The coflow velocity is parametrically varied. The methane-air chemistry is modeled using a fairly detailed mechanism that contains 81 elementary reactions and 24 species. Validation of the computational model is provided through comparisons of predictions with nonintrusive measurements. The combustion proceeds in two reaction zones, one a rich premixed zone and the other a nonpremixed zone. These reaction zones are spatially separated, but involve strong interactions between them due to thermochemistry and scalar transport. The fuel is mostly consumed in the premixed zone to produce CO and H2, which are transported to and consumed in the nonpremixed zone. The nonpremixed zone in turn provides heat and H-atoms to the premixed zone. For the range of conditions investigated, the zero-g partially premixed flames exhibit a stable behavior and a remarkably strong resistance to perturbations. In contrast, the corresponding normal-gravity flames exhibit oscillatory behavior at low coflow velocities but a stable behavior at high coflow velocities, and the behavior can be explained in terms of a global and convective instabilities. The effects of coflow and gravity on the flames are characterized through a parameter VR, defined as the ratio of coflow velocity to jet velocity. For VR ≤ 1 (low coflow velocity regime), the structures of both 0- and 1-g flames are strongly sensitive to changes in VR, while they are only mildly affected by coflow in the high coflow velocity regime (VR > 1). In addition, the spatio-temporal characteristics of the 0- and 1-g flames are markedly different in the first regime, but are essentially similar in the second regime. A more significant difference in the first regime between these flames is the presence of a flow instability that manifests itself through the self-excited oscillations of the 1-g flame and the concomitant flickering of the nonpremixed reaction zone. For VR ≤ 1, as the coflow velocity is increased, the oscillation amplitude decreases and the oscillation frequency increases, both of which are in accord with previous experimental and computational results concerning 1-g jet diffusion flames. The modified conserved scalar approach is found to be effective in characterizing the flame structure and developing state relationships for both steady and unsteady partially premixed flames. This is demonstrated by the fact that the temperature as well as the major and minor species profiles follow similar state relationships in terms of the modified mixture fraction for the 0- and 1-g flames, even though these flames have markedly different spatio-temporal characteristics.
The local role of tumor necrosis factor alpha in the modulation of neutrophil function at sites of inflammation.

OBJECTIVE To examine the hypothesis that tumor necrosis factor alpha (TNF-alpha) is an important local modulator of neutrophil function in the inflammatory microenvironment. DESIGN In vitro studies of host defense. PATIENTS A volunteer sample of healthy subjects. INTERVENTION Exudative neutrophils were collected from skin-blister chambers and functionally compared with blood neutrophils. METHODS Tumor necrosis factor alpha levels at sites of inflammation and neutrophil exudation were determined and compared with serum concentrations. Flow cytometry was used to evaluate neutrophil microbicidal activity and N-formyl-methionyl-leucyl-phenylalanine-induced changes in intracellular calcium and superoxide production. In vitro TNF-alpha was used to evaluate the nature and dose response of TNF-alpha-induced changes in neutrophil function. RESULTS Exudative neutrophils have an increased responsiveness to subsequent N-formyl-methionyl-leucyl-phenylalanine stimulation, as determined by changes in intracellular calcium. Microbicidal activity and superoxide production are also up-regulated compared with circulating neutrophils. The exudative microenvironment contains TNF-alpha at local levels that are capable of significantly enhancing neutrophil host defense. CONCLUSIONS Tumor necrosis factor alpha may serve to enhance neutrophil function at sites of inflammation. Neutrophils become more cytotoxic and have an enhanced ability to respond to weak environmental signals.
Leg mass characteristics of accurate and inaccurate kickers – an Australian football perspective

Abstract Athletic profiling provides valuable information to sport scientists, assisting in the optimal design of strength and conditioning programmes. Understanding the influence these physical characteristics may have on the generation of kicking accuracy is advantageous. The aim of this study was to profile and compare the lower limb mass characteristics of accurate and inaccurate Australian footballers. Thirty-one players were recruited from the Western Australian Football League to perform ten drop punt kicks over 20 metres to a player target. Players were separated into accurate (n = 15) and inaccurate (n = 16) groups, with leg mass characteristics assessed using whole body dual energy x-ray absorptiometry (DXA) scans. Accurate kickers demonstrated significantly greater relative lean mass (P ≤ 0.004) and significantly lower relative fat mass (P ≤ 0.024) across all segments of the kicking and support limbs, while also exhibiting significantly higher intra-limb lean-to-fat mass ratios for all segments across both limbs (P ≤ 0.009). Inaccurate kickers also produced significantly larger asymmetries between limbs than accurate kickers (P ≤ 0.028), showing considerably lower lean mass in their support leg. These results illustrate a difference in leg mass characteristics between accurate and inaccurate kickers, highlighting the potential influence these may have on technical proficiency of the drop punt.
Clinical outcomes of untreated symptomatic patients with negative findings on sonography of the thigh for deep vein thrombosis: our experience and a review of the literature.

OBJECTIVE Our objective was to determine whether immediate venography or other additional imaging is necessary in symptomatic patients who have negative findings on sonography of the thigh for deep vein thrombosis (DVT). MATERIALS AND METHODS We retrospectively evaluated the clinical outcomes of 146 patients with physical signs or symptoms consistent with DVT in whom sonography of the thigh was negative for DVT. We combined our results with those of three prospective studies that evaluated symptomatic patients with suspected DVT in whom sonography of the thigh had negative findings. Propagated DVT (from calf to thigh) and pulmonary emboli were considered adverse outcomes. RESULTS Only one pulmonary embolus (0.7%) occurred in our patient population. However, one (7.7%) of 13 patients who underwent second examinations because of persistent symptoms developed thigh DVT. Review of the literature found four (0.2%) of 1797 patients subsequently developed pulmonary emboli after undergoing sonography of the thigh that was initially interpreted as having negative findings. Fifteen (12.5%) of 120 patients who underwent second sonographic examinations developed DVT of the thigh. No deaths from pulmonary emboli occurred in patients in our study or patients in the studies published in the medical literature. CONCLUSION Immediate venography or other additional imaging is not necessary in symptomatic patients in whom sonography of the thigh is negative for DVT, given the exceedingly low risk of a pulmonary embolus. Follow-up sonography is indicated in persistently symptomatic patients to detect propagation of calf DVT into the thigh.
Corticosterone, Avoidance of Novelty, Risk-Taking and Aggression in a Wild Bird: No Evidence for Pleiotropic Effects

Certain inherent characteristics of individuals can determine both physiological and behavioural responses to environmental challenges, which could drive a correlation between levels of corticosterone (CORT), the most important stress hormone and behavioural profiles. Therefore, CORT level may mediate consistent behaviours along the shy/bold continuum, and thus, it could serve as a pleiotropic basis for behavioural syndromes. Moreover, behavioural responses to environmental challenges may have consequences for CORT concentrations, which would also result in a correlation between physiology and behaviours even without requiring pleiotropic mechanisms. Accordingly, we investigated the relationship between CORT and behaviour in free-living male collared flycatchers, Ficedula albicollis, using recently developed field assays. More specifically, we characterised novel object avoidance, intraspecific aggression and risk-taking in males and related these correlated behaviours to the concentration of CORT metabolites in droppings measured by enzyme immunoassay. Individuals with higher levels of excreted CORT metabolites had no consistently higher or lower behavioural scores along the shy/ bold spectrum, as avoidance of novelty, aggression and risk-taking were not systematically related to CORT metabolite concentrations in the same direction. Moreover, environmental challenges owing to the presence of a novel object, territorial intruder and a potential predator caused no elevation in the level of CORT metabolites. Therefore, we did not find correlative evidence for CORT driving correlated behaviours through pleiotropic effects or for particular behaviours during courtship causing elevation in CORT levels.
Prevalence and incidence of primary biliary cirrhosis are increasing in Finland

Objective. To examine the epidemiology of primary biliary cirrhosis (PBC) in Finland and to evaluate whether the possible increase in prevalence was attributable to the increasing incidence, better survival, or both. Material and methods. The Hospital Discharge Register, pathology registers, and death certificates for the years 1988–99 were scrutinized, and the patients identified were followed-up for survival until 31 October 2004. The study area covered four university hospital districts: a total of 25 hospitals. The diagnosis of PBC was regarded as definite (or probable) if three (or two) of the following criteria were fulfilled: positive antimitochondrial antibodies, constantly elevated alkaline phosphatase, and compatible liver histology. Results. In the total population of the study areas, the age-standardized prevalence of PBC increased during the study period from 103 (95% CI: 97–110) to 180 (172–189) per million inhabitants. Incidence increased from 12 (10–14) to 17 (15–20) per million inhabitants per year. The annual average increase in prevalence was 5.1% (4.2–5.9%, p<0.0001) and in incidence 3.5% (0.9%–6.0%, p=0.008). In gender-specific analyses among women, the prevalence of PBC increased from 161 (151–171) to 292 (277–207) per million during the study period and the incidence from 20 (16–24) to 27 (23–32) per million per year. The death rate was 4% per year and half the deaths were from liver-related causes. Survival after diagnosis during the study period lengthened. Conclusions. The prevalence of PBC increased in Finland during 1988–99, owing to both the increased incidence and the prolonged survival.
The Elements of Statistical Learning

Chapter 11 includes more case studies in other areas, ranging from manufacturing to marketing research. Chapter 12 concludes the book with some commentary about the scienti c contributions of MTS. The Taguchi method for design of experiment has generated considerable controversy in the statistical community over the past few decades. The MTS/MTGS method seems to lead another source of discussions on the methodology it advocates (Montgomery 2003). As pointed out by Woodall et al. (2003), the MTS/MTGS methods are considered ad hoc in the sense that they have not been developed using any underlying statistical theory. Because the “normal” and “abnormal” groups form the basis of the theory, some sampling restrictions are fundamental to the applications. First, it is essential that the “normal” sample be uniform, unbiased, and/or complete so that a reliable measurement scale is obtained. Second, the selection of “abnormal” samples is crucial to the success of dimensionality reduction when OAs are used. For example, if each abnormal item is really unique in the medical example, then it is unclear how the statistical distance MD can be guaranteed to give a consistent diagnosis measure of severity on a continuous scale when the larger-the-better type S/N ratio is used. Multivariate diagnosis is not new to Technometrics readers and is now becoming increasingly more popular in statistical analysis and data mining for knowledge discovery. As a promising alternative that assumes no underlying data model, The Mahalanobis–Taguchi Strategy does not provide suf cient evidence of gains achieved by using the proposed method over existing tools. Readers may be very interested in a detailed comparison with other diagnostic tools, such as logistic regression and tree-based methods. Overall, although the idea of MTS/MTGS is intriguing, this book would be more valuable had it been written in a rigorous fashion as a technical reference. There is some lack of precision even in several mathematical notations. Perhaps a follow-up with additional theoretical justi cation and careful case studies would answer some of the lingering questions.
Intonation contrast in Cantonese speakers with hypokinetic dysarthria associated with Parkinson's disease.

PURPOSE Speech produced by individuals with hypokinetic dysarthria associated with Parkinson's disease (PD) is characterized by a number of features including impaired speech prosody. The purpose of this study was to investigate intonation contrasts produced by this group of speakers. METHOD Speech materials with a question-statement contrast were collected from 14 Cantonese speakers with PD. Twenty listeners then classified the productions as either questions or statements. Acoustic analyses of F0, duration, and intensity were conducted to determine which acoustic cues distinguished the production of questions from statements, and which cues appeared to be exploited by listeners in identifying intonational contrasts. RESULTS The results show that listeners identified statements with a high degree of accuracy, but the accuracy of question identification ranged from 0.56% to 96% across the 14 speakers. The speakers with PD used similar acoustic cues as nondysarthric Cantonese speakers to mark the question-statement contrast, although the contrasts were not observed in all speakers. Listeners mainly used F0 cues at the final syllable for intonation identification. CONCLUSION These data contribute to the researchers' understanding of intonation marking in speakers with PD, with specific application to the production and perception of intonation in a lexical tone language.
ISRS BRIEFING PAPER 3 THE EFFECTS OF TERRESTRIAL RUNOFF OF SEDIMENTS , NUTRIENTS AND OTHER POLLUTANTS ON CORAL REEFS

Increasing terrestrial runoff of sediments, nutrients and other pollutants into the sea is a growing concern for many of the over 100 nations endowed with coral reefs. This document provides a brief overview of the known effects of exposure to terrestrial runoff on the health of corals and of coral reef ecosystems. It also describes measures some countries have started taking, as there are considerable economic net benefits gained from an investment into reducing the loss of sediments, nutrients and other pollutants into the sea.
Assessing Problematic States in Patients' Narratives: The Grid of Problematic States

The authors present the theoretical background, development, and validation of a new psychotherapy process rating tool: Grid of Problematic States (GPS). The GPS is based on Horowitz's states of mind theory, which describes recurrent patterns of experience and behavior. Meaningful changes in the observed states indicate therapeutic change. The GPS is designed for use with transcripts from psychotherapy sessions and focuses on narrative episodes within the patient dialogue. The GPS was applied to a completely transcribed cognitive psychotherapy with a patient diagnosed as mild major depressive. The authors demonstrated that the GPS could reliably assess disorganization and the development of stable construct clusters of thought themes, emotions, and somatic sensations. The interpretation of results is consistent with the patient's clinical assessment.
Acute Paraspinal Muscle Compartment Syndrome Treated with Surgical Decompression

A 25-year-old man who went surfboarding every weekend had left low back pain for several months. Bed rest and analgesics relieved the pain, and he did not seek treatment for his condition. After a day of surfboarding, he suffered severe low back pain during the night and was taken to the emergency department of the local hospital. The patient denied having had any traumatic episode or previous severe pain. At the emergency department, laboratory data could not be obtained because of lack of equipment. The pain was somewhat reduced by a caudal block and the intravenous administration of pentazocine. The next morning, however, the patient still had severe low back pain and was transferred to our hospital for a more detailed examination. Physical findings on admission showed a tenderness point at the left lumbar paraspinal muscle and decreased sensation in the left lumbosacral area. Laboratory findings (with normal ranges in parentheses) were as follows: hemoglobin, 13.1 g/dl (14.0 to 17.5); white blood-cell count, 8.6 10/L (4.5 to 11); platelets, 248 10/ l (150 to 450); total bilirubin, 1.1 mg/dl (0.3 to 1.2); blood urea nitrogen, 9 mg/dl (8 to 23); creatinine, 0.8 mg/dl (0.1 to 0.4); aspartate aminotransferase, 193 IU/L (10 to 48); alanine aminotransferase, 41 IU/L (10 to 40); lactate dehydrogenase, 505 IU/L (50 to 200); amylase, 39 SU/dl (25 to 85 U/L); creatine kinase, 21,440 IU/L (50 to 200); c-reactive protein, 0.1 mg/dl (0.3); and elevated urinary myoglobin. A T2-weighted MRI scan in the axial plane showed a homogeneous signal increase consistent with left paraspinal muscle edema (Fig. 1). Lumbar disc disruption was ruled out by a T2-weighted MRI scan in the sagittal plane (Fig. 2). Paraspinal muscle compartment syndrome was suspected. Initially, the patient was treated with bed rest and intravenous administration of analgesics because his pain was slightly diminished and under control. The next day, however, his laboratory data were worse, and his creatine kinase level was 34,692 IU/L. His condition did not improve,