Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling of Spatio-temporal Zero Truncated Patterns in Infectious Disease Surveillance Data

This paper is motivated by spatio-temporal pattern in the occurrence of Leishmaniasis in Afghanistan and the relatively high number of zero counts. We hold the view that correlations that arise from spatial and temporal sources are inherently distinct. Our method decouples these two sources of correlations, there are at least two advantages in taking this approach. First, it circumvents the need to inverting a large correlation matrix, which is a commonly encountered problem in spatio-temporal analyses. Second, it simplifies the modelling of complex relationships such as anisotropy, which would have been extremely difficult or impossible if spatio-temporal correlations were simultaneously considered. We identify three challenges in the modelling of a spatio-temporal process: (1) accommodation of covariances that arise from spatial and temporal sources; (2) choosing the correct covariance structure and (3) extending to situations where a covariance is not the natural measure of association. Moreover, because the data covers a period that overlaps with the US invasion of Afghanistan, the high number of zero counts may be the result of no disease incidence or lapse of data collection. To resolve this issue, a model truncated at zero built on a foundation of the generalized estimating equations was proposed.
Method Development for Measuring Biodegradable Dissolved Organic Nitrogen in Treated Wastewater

A method for determining biodegradable dissolved organic nitrogen (BDON) in treated wastewater was developed. The method adopts the approaches used in the biochemical oxygen demand and biodegradable dissolved organic carbon tests to make it usable as a routine procedure at wastewater treatment plants (WWTPs). The development focused on various aspects of the procedure, including inoculum type and concentration, incubation period, and the need for sample filtration after incubation. The method was tested with filtered effluent samples from two nutrient removal WWTPs and standard organic nitrogen solutions. Accurate and precise BDON results were obtained with 2 mL of acclimated mixed‐liquor suspended solids diluted to a concentration of 240 mg/L as an inoculum and an incubation period of 20 days. Sample filtration after incubation was not required.
Song Performance Rules in the Oriental Magpie Robin (Copsychus salauris)

of the thrush family (Turdidae) are renowned for a quite melodious but nevertheless complex mode of singing. Such holds true also for the Oriental Magpie Robin (Copsychus saularis) that settles in some tropical regions of Asia. We have studied the territorial singing of this species in the area of Biratnagar (Nepal), and present a list of first results here. Analysis of singing episodes of (duration ~ 40 min each) recorded from adult males (n=5) who were flagging their territories at the beginning of their breeding season (March 2007), yielded three sets of findings: (1) oriental magpie robins resemble some song performance rules of other thrushes, and such concern especially the time domain. (2) However, some interesting idiosyncracy were found as well. This was true, for instance, for the robins' repetitive singing style and their mode of motif type combination within and also across songs. (3) In addition, it was remarkable that neighbours did not share parts of their repertoires. These findings contribute to the discussion of two aspects; namely the use of 'song as an interactive tool' and the role of 'learning as an origin of pattern similarity'.
Suspended liquid particle disturbance on laser-induced blast wave and low density distribution

The impurity effect of suspended liquid particles on the laser-induced gas breakdown was experimentally investigated in quiescent gas. The focus of this study is the investigation of the influence of the impurities on the shock wave structure as well as the low density distribution. A 532 nm Nd:YAG laser beam with an 188 mJ/pulse was focused on the chamber filled with suspended liquid particles 0.9 ± 0.63 μm in diameter. Several shock waves are generated by multiple gas breakdowns along the beam path in the breakdown with particles. Four types of shock wave structures can be observed: (1) the dual blast waves with a similar shock radius, (2) the dual blast waves with a large shock radius at the lower breakdown, (3) the dual blast waves with a large shock radius at the upper breakdown, and (4) the triple blast waves. The independent blast waves interact with each other and enhance the shock strength behind the shock front in the lateral direction. The triple blast waves lead to the strongest shock wave in .
Analysis of Hamster Tumor Cell Lines Isolated from Single Colonies Soon After Induction by Polyoma Strains Differing in Transplant Antigen Production

Tumor cell colonies, arising after the infection of hamster embryo cells with two strains of polyoma virus (PV) which differed in their capacity to induce the PV-specific transplant antigen, were isolated and studied for their transplant and tumor or “T” antigen content and growth characteristics in vitro and in vivo. Four of four tumor lines induced by the transplant immunogenic 3049 strain contained the transplant antigen, while only one of seven lines induced by the immunogenically deficient sp-D strain showed direct evidence for this antigen. T antigen was not detected by immunofluorescence in three tumor lines induced by the 3049 virus which contained the polyoma transplant antigen. No differences in growth capacity on plastic, in agar, or in the hamster subcutaneous tissue were apparent in spite of significant differences in transplant antigen content among the clones.
Alterations in protein kinase A and protein kinase C levels in heart failure due to genetic cardiomyopathy.

BACKGROUND It is becoming evident that both cardiac and skeletal muscles are affected in congestive heart failure. Although protein kinases are known to regulate cardiac function, very little is known about their status in cardiac and skeletal muscles during the development of congestive heart failure. OBJECTIVE To determine changes in the activities and protein levels of protein kinase A (PKA) and protein kinase C (PKC) in cardiac and skeletal muscles in congestive heart failure due to genetic cardiomyopathy on the basis that PKA and PKC are crucial for protein phosphorylation. ANIMALS AND METHODS Genetically cardiomyopathic UM-X7.1 hamsters (250 to 300 days old) and age-matched Syrian hamsters were used in this study. PKA and PKC activities were assayed by measuring 32P from [gamma-32P]ATP incorporated into synthetic substrates. Relative protein contents of these protein kinases were obtained by using immunoblot analysis in control and failing hamster hearts and skeletal muscles. RESULTS PKC activity was significantly increased in the failing hearts compared with control preparations. The relative protein contents of cytosolic PKC-alpha and -epsilon , and of particulate PKC-epsilon isozymes were significantly increased in failing hearts. PKC activity was also markedly increased in cardiomyopathic skeletal muscle. Furthermore, PKA activity and protein level in both cardiac and skeletal muscles were significantly increased in the failing heart group compared with control values. CONCLUSIONS Increased PKC activity in heart failure may be due to changes in PKC-alpha and -epsilon isozymes in cardiomyopathic hearts. Alterations of PKA and PKC in congestive heart failure were not limited to the heart because similar changes in enzyme activities were evident in skeletal muscle.
A pooled data analysis on the use of intermittent cyclical etidronate therapy for the prevention and treatment of corticosteroid induced bone loss.

OBJECTIVE To conduct a pooled data analysis in a group of patients defined by sex, menopausal status, and underlying disease in order to examine the effect of intermittent cyclical etidronate in the prevention and treatment of corticosteroid induced osteoporosis. METHODS We selected 5 randomized, placebo controlled studies that examined the efficacy of intermittent cyclical etidronate therapy in which the raw data were available for analysis. Three were prevention studies and 2 treatment studies. The primary outcome was the difference between treatment groups in the percentage change from baseline in lumbar spine bone density. Secondary outcomes included the difference between treatment groups in the percentage change from baseline in femoral neck and trochanter bone density, and vertebral fracture rates. RESULTS Results are separately pooled for the prevention and treatment studies. The prevention studies had significant mean differences (95% CI) between groups in mean percentage change from baseline in lumbar spine, femoral neck, and trochanter bone density of 3.7 (2.6 to 4.7), 1.7 (0.4 to 2.9), and 2.8% (1.3 to 4.2) after one year of treatment, in favor of the etidronate group. The treatment studies displayed a mean difference between groups in mean percentage change from baseline in lumbar spine bone density of 4.8 (2.7 to 6.9) and 5.4% (2.5 to 8.4) after one and 2 years of therapy. In the prevention studies, a reduced fracture incidence was observed in the etidronate group compared with the placebo group (relative risk 0.50; CI 0.21 to 1.19). CONCLUSION Etidronate therapy was effective in preventing bone loss in the prevention studies and in preventing or slightly increasing bone mass in the treatment studies. A fracture benefit was observed in postmenopausal women treated with etidronate in the prevention studies.
DETERMINATION OF PHENOBARBITAL IN HUMAN PLASMA BY A SPECIFIC LIQUID CHROMATOGRAPHY METHOD: APPLICATION TO A BIOEQUIVALENCE STUDY

A liquid chromatography method was developed and validated for the determination of phenobarbital in human plasma using phenytoin as internal standard. The drugs were extracted from plasma by liquid-liquid extraction and separated isocratically on a C12 analytical column, maintained at 35 oC, with water:acetonitrile:methanol (58.8:15.2:26, v/v/v) as mobile phase, run at a flow rate of 1.2 mL/min with detection at 205 nm. The method was linear in the range of 0.1-4 μg/mL (r2=0.9999) and demonstrated acceptable results for the precision, accuracy and stability studies. The method was successfully applied for the bioequivalence study of two tablet formulations (test and reference) of phenobarbital 100 mg after single oral dose administration to healthy human volunteers.
Sarcomatoid Carcinomas of the Upper Aerodigestive Tracts

Summary: Sarcomatoid carcinoma of the upper aerodigestive tract continues to be one of the most difficult diagnostic challenges for surgical pathologists. Histogenesis has been settled in favor of a divergent (mesenchymal) differentiation of a carcinoma, most often a squamous cell carcinoma. Finding the carcinoma and/or its immunohistochemical marker in the metaplastic cells establishes the diagnosis. There are, however, lesions that can simulate sarcomatoid carcinomas to varying degrees, and in which neither a definable carcinoma nor immunohistochemical evidence of one can be found. Such lesions fall into several categories: 1. benign reactive lesions, 2. inflammatory myofibroblastic tumors, 3. sarcomas, usually low‐grade, 4. atypical pseudosarcomatous proliferation. The clinicopathologic considerations of sarcomatoid carcinomas are presented in this context and include immunohistochemical findings, prognostic factors, and biologic course.
Simultaneous bilateral total hip arthroplasty in sickle cell disease.

Simultaneous bilateral uncemented total hip arthroplasty for avascular necrosis of the femoral head resulting from sickle cell disease was performed in 18 consecutive patients (36 hips). The patients were followed 2 to 10 years (mean, 5.7 years). All patients showed improvement in postoperative hip scores compared with preoperative scores for pain, range of motion, and function. There were 2 immediate postoperative complications related to sickling of red blood cells. One intraoperative fracture of the proximal femur occurred. There was 1 superficial and 1 deep infection. There was no femoral stem loosening, but 1 protrusio acetabuli occurred. One acetabular cup was revised for instability. Heterotopic ossification developed in 2 patients. Simultaneous bilateral total hip arthroplasty in sickle cell disease is a good option in a select group of patients with adequate hydration and ventilation in the perioperative and postoperative periods.
Use of a Comprehensive Geriatric Assessment for the Management of Elderly Patients With Advanced Non-Small-Cell Lung Cancer: The Phase III Randomized ESOGIA-GFPC-GECP 08-02 Study.

PURPOSE Comprehensive geriatric assessment (CGA) is recommended to assess the vulnerability of elderly patients, but its integration in cancer treatment decision making has never been prospectively evaluated. Here, in elderly patients with advanced non-small-cell lung cancer (NSCLC), we compared a standard strategy of chemotherapy allocation on the basis of performance status (PS) and age with an experimental strategy on the basis of CGA. PATIENTS AND METHODS In a multicenter, open-label, phase III trial, elderly patients ≥ 70 years old with a PS of 0 to 2 and stage IV NSCLC were randomly assigned between chemotherapy allocation on the basis of PS and age (standard arm: carboplatin-based doublet if PS ≤ 1 and age ≤ 75 years; docetaxel if PS = 2 or age > 75 years) and treatment allocation on the basis of CGA (CGA arm: carboplatin-based doublet for fit patients, docetaxel for vulnerable patients, and best supportive care for frail patients). The primary end point was treatment failure free survival (TFFS). Secondary end points were overall survival (OS), progression-free survival, tolerability, and quality of life. RESULTS Four hundred ninety-four patients were randomly assigned (standard arm, n = 251; CGA arm, n = 243). Median age was 77 years. In the standard and CGA arms, 35.1% and 45.7% of patients received a carboplatin-based doublet, 64.9% and 31.3% received docetaxel, and 0% and 23.0% received best supportive care, respectively. In the standard and CGA arms, median TFFS times were 3.2 and 3.1 months, respectively (hazard ratio, 0.91; 95% CI, 0.76 to 1.1), and median OS times were 6.4 and 6.1 months, respectively (hazard ratio, 0.92; 95% CI, 0.79 to 1.1). Patients in the CGA arm, compared with standard arm patients, experienced significantly less all grade toxicity (85.6% v 93.4%, respectively P = .015) and fewer treatment failures as a result of toxicity (4.8% v 11.8%, respectively; P = .007). CONCLUSION In elderly patients with advanced NSCLC, treatment allocation on the basis of CGA failed to improve the TFFS or OS but slightly reduced treatment toxicity.
MISC: A data set of information-seeking conversations

Conversational interfaces to information retrieval systems, via software agents such as Siri or Cortana, are of commercial and research interest. To build or evaluate these software interfaces it is natural to consider how people act in the same role, but there is little public, fine-grained, data on interactions with intermediaries for web tasks. We introduce the Microsoft Information-Seeking Conversation data (MISC), a set of recordings of information-seeking conversations between human “seekers” and “intermediaries”. MISC includes audio and video signals; transcripts of conversation; affectual and physiological signals; recordings of search and other computer use; and post-task surveys on emotion, success, and effort. We hope that these recordings will support conversational retrieval interfaces both in engineering (how can we make “natural” systems? ) and evaluation (what does a “good” conversation look like? ).
AMINOGLYCOSIDE OTOTOXICITY IN THE HUMAN

One hundred thirty‐eight patient courses of tobramycin (tobra) and gentamicin (genta) were prospectively monitored for ototoxicity using weekly audiograms and electronystag‐mograms. Twice weekly drug serum levels and kidney function tests were determined. A pre, during, and post‐therapy history was obtained and the results were analyzed to determine significant parameters of ototoxicity.
Mammalian enzymatic repair of etheno and para-benzoquinone exocyclic adducts derived from the carcinogens vinyl chloride and benzene.

Two human carcinogens that have been extensively studied are vinyl chloride and benzene. The active metabolites used in this study are chloroacetaldehyde (CAA) and para-benzoquinone (pBQ). Each forms exocyclic adducts between the N1 and N6 of A, the N3 and N4 of C and the N1 and N2 of G. Only CAA has been found to form the N2,3 adduct of G. CAA and pBQ adducts differ structurally in size and in the number of added rings, pBQ adding two rings to the base, while etheno bases have a single five-membered ring. The mechanism of repair of these two types of adducts by human enzymes has been studied in our laboratory with defined oligodeoxynucleotides and a site-specific adduct. The etheno derivatives are repaired by DNA glycosylase activity; two mammalian glycosylases are responsible: alkylpurine-DNA-N-glycosylase (APNG) and mismatch-specific thymine-DNA glycosylase. The former repairs 1,N6-ethenoA (epsilon A) as rapidly as the original substrate, 3-methyladenine, while the latter repairs 3,N4-ethenoC (epsilon C) more efficiently than the G/T mismatch. Our finding that there are separate enzymes for epsilon A and epsilon C has been confirmed by the use of tissue extracts from an APNG knockout mouse. As pBQ is much less efficient than CAA in modifying bases, the biochemical studies required total synthesis of the nucleosides. Furthermore, the pBQ adduct-containing oligomers are cleaved, to various extents by a different class of enzyme: human and bacterial N-5'-alkylpurine (AP) endonucleases. The enzyme incises such oligomers 5' to the adduct and generates 3'-hydroxyl and 5'-phosphoryl termini but leaves the modified base on the 5'-terminus of the 3' cleavage fragment ('dangling base'). Using active-site mutants of the human AP endonuclease, we found that the active site for the primary substrate, abasic (AP) site, is the same as that for the bulky pBQ adducts. There appears to be no clear rationale for the widely differing recognition and repair mechanisms for these exocyclic adducts, as shown for the repair of the same types of modification on different bases (e.g. epsilon A and epsilon C) and for completely unrelated lesions (e.g. AP site and pBQ adducts). Another important variable that affects the rate and extent of repair is the effect of neighbouring bases. In the case of epsilon A, this sequence-dependent repair correlates with the extent of double-strandedness of the substrate, as demonstrated by thermal stability studies.
Phorbol ester‐induced degranulation in adherent human eosinophil granulocytes is dependent on CD11/CD18 leukocyte integrins

Secretion of unique eosinophil granule constituents may play a role in allergic and parasitic reactions. Therefore we have investigated possible mechanisms for regulation of secretion in eosinophils. A hemolytic plaque assay and an enzyme‐linked immu‐nospot (ELISPOT) assay were developed for detection of secreted eosinophil cationic protein (ECP) from single adherent eosinophils. The protein kinase C activator phorbol 12‐myristate 13‐acetate (PMA) induced release of ECP in a dose‐dependent fashion but 4‐αPMA, an analogue that does not activate protein kinase C, did not cause degranulation. Staurosporin and K252a, inhibitors of protein kinase C, decreased PMA‐induced ECP secretion. Low concentrations of cytochalasin B enhanced PMA‐induced secretion but high concentrations had an inhibitory effect. The calcium ionophores A23187 and ionomycin were weaker secretagogues than PMA. Tumor necrosis factor, granulocyte‐macrophage colony‐stimulating factor, interleukin‐3, interleukin‐5, N‐formylmeth‐ionyl‐leucyl‐phenylalanine, and lipopolysaccharide caused little or no degranulation in adherent eosinophils. Preincubation of eosinophils with antibodies to CD18, the common β chain of leukocyte adhesion proteins, resulted in inhibition of PMA‐induced ECP release from adherent cells. l,2‐Bis(O‐aminophenyl)ethane‐ethane‐N,N,N,N′‐tet‐raacetic acid (BAPTA), an agent that acts intracellularly by chelation of calcium, also inhibited PMA‐mediated ECP release. In conclusion, PMA induces release of ECP from single adherent eosinophils and the effect appears to be mediated via protein kinase C and, in contrast to that in neutrophils, to be dependent on CD11/CD18 leukocyte integrins.
Growth Differentiation Factor 15 Mediates Systemic Glucose Regulatory Action of T-Helper Type 2 Cytokines

T-helper type 2 (Th2) cytokines, including interleukin (IL)-13 and IL-4, produced in adipose tissue, are critical regulators of intra-adipose and systemic lipid and glucose metabolism. Furthermore, IL-13 is a potential therapy for insulin resistance in obese mouse models. Here, we examined mediators produced by adipocytes that are responsible for regulating systemic glucose homeostasis in response to Th2 cytokines. We used RNA sequencing data analysis of cultured adipocytes to screen factors secreted in response to recombinant IL-13. Recombinant IL-13 induced expression of growth differentiation factor 15 (GDF15) via the Janus kinase-activated STAT6 pathway. In vivo administration of α-galactosylceramide or IL-33 increased IL-4 and IL-13 production, thereby increasing GDF15 levels in adipose tissue and in plasma of mice; however, these responses were abrogated in STAT6 knockout mice. Moreover, administration of recombinant IL-13 to wild-type mice fed a high-fat diet (HFD) improved glucose intolerance; this was not the case for GDF15 knockout mice fed the HFD. Taken together, these data suggest that GDF15 is required for IL-13–induced improvement of glucose intolerance in mice fed an HFD. Thus, beneficial effects of Th2 cytokines on systemic glucose metabolism and insulin sensitivity are mediated by GDF15. These findings open up a potential pharmacological route for reversing insulin resistance associated with obesity.
Therapy of spontaneous ringworm in cats with orally administered griseofulvin.

Ringworm in cats is a common dermatological disorder of public health importance. Investigations in this country 3,7 and other parts of the world 5,6 have disclosed that Microsporum canis is the principal cause of this condition in cats. In a recent survey 3 of ringworm of animals in the United States, this fungus has been found to be responsible for approximately 98% of the feline cases studied. Such infections are frequently transmitted to human contacts, and infected cats constitute the principal source of this agent for man. M. canis is also an important cause of dermatophytosis in dogs, pet monkeys, and horses, 3 and such lower-animal hosts are also frequently involved in the transmission of the disease to humans. Although it has been conclusively established that the relatively common M. canis ringworm in man represents spread from cats and other animals, to date no attempts have been made in this