Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic analysis of human immunodeficiency virus type 1 strains from patients in Cyprus: identification of a new subtype designated subtype I

DNA sequences encoding the C2 to V3 region of envelope glycoprotein gp120 of human immunodeficiency virus type 1 (HIV-1) were amplified by PCR from uncultured peripheral blood mononuclear cells obtained from 24 of 25 HIV-1-seropositive patients from Cyprus. By using a heteroduplex mobility assay (HMA), all amplified products were studied genetically and compared with 16 previously characterized HIV-1 strains belonging to subtypes A through F. HMA results revealed that HIV-1 gp120 sequences from 15 of our patients were of subtype B of HIV-1, whereas one isolate was of subtype C. However, gp120 sequences from eight patients had no obvious similarities to the known subtypes as defined by HMA. DNA sequencing and phylogenetic analyses of molecular clones confirmed the HMA results and placed the eight undefined HIV-1 isolates into three distinct genetic clusters. On the basis of branch topology and lengths of the phylogenetic tree, we conclude that one group consisting of three clones from two patients represents a new HIV-1 env subtype, which we have termed subtype I. The remaining two sequence clusters, consisting of five sequences from four patients and two sequences from two other patients, are distally related to subtypes A and F. These data demonstrate the extensive heterogeneity of HIV-1 in Cyprus, including the presence of new subtype.
High-resolution inversion of OMI formaldehyde columns to quantify isoprene emission on ecosystem-relevant scales: application to the southeast US

Abstract. Isoprene emissions from vegetation have a large effect on atmospheric chemistry and air quality. “Bottom-up” isoprene emission inventories used in atmospheric models are based on limited vegetation information and uncertain land cover data, leading to potentially large errors. Satellite observations of atmospheric formaldehyde (HCHO), a high-yield isoprene oxidation product, provide “top-down” information to evaluate isoprene emission inventories through inverse analyses. Past inverse analyses have however been hampered by uncertainty in the HCHO satellite data, uncertainty in the time- and NO x -dependent yield of HCHO from isoprene oxidation, and coarse resolution of the atmospheric models used for the inversion. Here we demonstrate the ability to use HCHO satellite data from OMI in a high-resolution inversion to constrain isoprene emissions on ecosystem-relevant scales. The inversion uses the adjoint of the GEOS-Chem chemical transport model at 0.25 ∘ × 0.3125 ∘ horizontal resolution to interpret observations over the southeast US in August–September 2013. It takes advantage of concurrent NASA SEAC 4 RS aircraft observations of isoprene and its oxidation products including HCHO to validate the OMI HCHO data over the region, test the GEOS-Chem isoprene oxidation mechanism and NO x environment, and independently evaluate the inversion. This evaluation shows in particular that local model errors in NO x concentrations propagate to biases in inferring isoprene emissions from HCHO data. It is thus essential to correct model NO x biases, which was done here using SEAC 4 RS observations but can be done more generally using satellite NO 2 data concurrently with HCHO. We find in our inversion that isoprene emissions from the widely used MEGAN v2.1 inventory are biased high over the southeast US by 40 % on average, although the broad-scale distributions are correct including maximum emissions in Arkansas/Louisiana and high base emission factors in the oak-covered Ozarks of southeast Missouri. A particularly large discrepancy is in the Edwards Plateau of central Texas where MEGAN v2.1 is too high by a factor of 3, possibly reflecting errors in land cover. The lower isoprene emissions inferred from our inversion, when implemented into GEOS-Chem, decrease surface ozone over the southeast US by 1–3 ppb and decrease the isoprene contribution to organic aerosol from 40 to 20 %.
Overlapping expression domains of bone morphogenetic protein family members potentially account for limited tissue defects in BMP7 deficient embryos

BMP7 is expressed at diverse sites in the developing mouse embryo, including visceral endoderm, notochord, heart, eye, kidney, and bone. A null mutation in BMP7 results in defects largely confined to the developing kidney and eye. To examine whether other bone morphogenetic protein (BMP) family members potentially substitute for BMP7 in mutant embryos, thereby restricting the observed defects, we analyzed the expression patterns of BMP2 through BMP7 in wild‐type and mutant tissues. In the central nervous system and heart, which develop normally in the absence of BMP7 signaling, expression domains of other BMP family members completely overlap with that of BMP7. The variable expressivity of the eye defect correlates with partially overlapping BMP4 and BMP7 expression domains during early eye induction. The loss of BMP7 signaling in the kidney results in apoptosis in the metanephric mesenchyme, a cell population that exclusively expresses BMP7. Thus, tissue defects observed in BMP7 deficient embryos are restricted to cell populations exclusively expressing BMP7. These data suggest that BMP family members can functionally substitute for BMP7 at sites where they colocalize in vivo. Dev. Dyn. 208:349–362, 1997. © 1997 Wiley‐Liss, Inc.
The ‘goatee’ of goatfish: innervation of taste buds in the barbels and their representation in the brain

Goatfish use a pair of large chin barbels to probe the sea bottom to detect buried prey. The barbels are studded with taste buds but little else is known about the neural organization of this system. We found that the taste buds of the barbel are innervated in a strict orthogonal fashion. The barbel is innervated by a main nerve trunk running in the core of the barbel. A longitudinal nerve bundle originates from the main trunk and, after running a short distance distally, divides into two circumferential nerve bundles (CNB) extending respectively, medially and laterally around the barbel. Approximately 15 CNBs innervate each 1 mm length of barbel. At each transverse level, the CNB innervates two clusters of taste buds, each containing 14 end–organs. The primary taste centre in the brain is similarly extraordinary. The sensory inputs from the barbel terminate in a derived dorsal facial lobe, which has a highly convoluted surface forming a multitude of tubercles. Electrophysiological mapping experiments show that the entire barbel is somatotopically represented in a recurved elongate tubular fashion within the dorsal facial lobe.
Identification of a proliferation signature related to survival in nodal peripheral T-cell lymphomas.

PURPOSE Nodal peripheral T-cell lymphomas (PTCLs) constitute a heterogeneous group of neoplasms, suggesting the existence of molecular differences contributing to their histologic and clinical variability. Initial expression profiling studies of T-cell lymphomas have been inconclusive in yielding clinically relevant insights. We applied DNA microarrays to gain insight into the molecular signatures associated with prognosis. MATERIALS AND METHODS We analyzed the expression profiles of 35 nodal PTCLs (23 PTCLs unspecified and 12 angioimmunoblastic) using two different microarray platforms, the cDNA microarray developed at the Spanish National Cancer Centre and an oligonucleotide microarray. RESULTS We identified five clusters of genes, the expression of which varied significantly among the samples. Genes in these clusters seemed to be functionally related to different cellular processes such as proliferation, inflammatory response, and T-cell or B-cell lineages. Regardless of the microarray platform used, overexpression of genes in the proliferation signature was associated significantly with shorter survival of patients. This proliferation signature included genes commonly associated with the cell cycle, such as CCNA, CCNB, TOP2A, and PCNA. Moreover the PTCL proliferation signature showed a statistically significant inverse correlation with clusters of the inflammatory response (P < .0001), as well as with the percentage of CD68(+) cells. CONCLUSION Our findings indicate that proliferation could be an important factor in evaluating nodal PTCL outcome and may help to define a more aggressive phenotype.
Virulence properties of diarrheagenic E. coli and etiology of diarrhea in infants, young children and other age groups in Southeast, Nigeria.

Diarrhoeal diseases constitute one of the most important causes of illness and death all over the world. In Nigeria, the epidemiology of diarrheagenic bacteria and the virulence of the various E. coli pathotypes have not been well studied because most of the currently published data were from the southwestern axis leaving the southeast and north unstudied. 520 stool samples were collected from infants, young children and other age groups with acute diarrhoeal diseases in Enugu and Onitsha, Southeastern Nigeria. Stool samples from 250 apparently healthy individuals with similar age distribution and locality were used as control subjects. The stool samples were screened for diarrhoeal causing bacterial agents. The isolated E. coli strains from both groups were examined by PCR for 16 virulence genes. Out of the 520 stool samples in the diarrhoea group, majority, 102 (44.74%) were Esherichia coli. Fifty (49.02%) were enteropathogenic (EPEC), 22 (21.57%) were enterotoxigenic (ETEC) while 7.84% was EAEC. Sex had no effect on the distribution of diarrhoegenic bacteria, except for EIEC. The isolated E. coli strains from the diarrhea and healthy asymptomatic age-matched control groups examined by PCR for 16 virulence genes indicates that the detection of EAEC, ETEC, EPEC and EIEC were significantly associated with diarrhea. The isolation of about eight different bacterial pathogens of diarrheogenic importance especially E. coli confirms the fact that these organisms play important role in the etiology of acute diarrhoea in Southeastern Nigeria. Routine surveillance especially for diarrheagenic E. coli, would be useful in identifying outbreaks and help in identifying potential reservoirs and transmission routes.
DeepHolo: recognizing 3D objects using a binary-weighted computer-generated hologram

Three-dimensions (3D) models contain a wealth of information about every object in our universe. However, it is difficult to semantically recognize the media forms, even when they featured in simplest form of objects. We propose the DeepHolo network using binary-weighted computer-generated holograms (CGHs) reconstructed from point cloud models. This neural network facilitates manipulation of 3D point cloud form, and allows it to be processed as Two-dimensions (2D) data. We construct the network using hologram data, which is simpler and contains smaller volume of information than their point cloud data(PCD) counterpart, leading to a smaller number of parameters required. The Deep Neural Network (DNN) is trained to recognize holograms of 3D objects, so that it resembles a point attributed to a 3D model of a similar object to the one depicted in the hologram. DeepHolo network allows high precision object recognition, as well as processing 3D data using much lesser computer resources. We evaluate our method on a recognition task space efficiency, and outperforming state-of-the-art methods.
Difficult mask ventilation made easy: Three cases of Parry Romberg syndrome

Parry Romberg syndrome presenting as hemifacial atrophy poses various perioperative problems due to multi-system involvement. These patients have several anaesthetic implications which are published as case reports. In spite of several case reports, airway issues associated with this disease is under-discussed. This report of three cases discusses airway difficulties and the multiple methods to tackle them in an easier way by focussing concentration on airway assessment and appropriate preoperative planning.
Country Image and Brand Equity Effects of Chinese Firms and Their Products on Developed-Market Consumer Perceptions

As China’s rapid economic growth continues to be a significant dimension of the world economy and international business, more Chinese multinational firms have been emerging with increasing efforts towards internationalization. While manufacturing, labor efficiency and costs have been a source of their competitive advantage, one area of relative weakness has been their lack of corporate/product brand equity and recognition. Coupled with potential negative country image effects, this deficiency has hindered a more positive perception and acceptance of brands and products from China, particularly in the more developed markets, such as the United States (U.S.). This empirical study examines the nature of such a challenge faced by Chinese firms and their need to develop an effective branding strategy for success in the U.S. market.
MULTI-PRODUCT EXPORTERS AND PRODUCT SWITCHING BEHAVIOUR OF NEW ZEALAND FIRMS

Using a unique dataset that covers (at 10 digit product codes) all exporting firms in New Zealand from 1997 to 2007, this paper analyzes the patterns of their product mix, how it changes over time and how this relates to firm characteristics. We suggest that looking at the relative importance of added and dropped products is as important as firm entry/exit in reallocation of resources. We find that product switching occurs frequently. It is also shown that dropping products is more likely to happen than adding products, suggesting the difficulty of entering new markets/products. We also show that products with a smaller share and tenure are more likely to be dropped by a firm. Finally, the link between volatility of earnings and the choice of product mix suggests that single product exporters are more stable. The results make a good case for product-firm characteristics being an important part of export decisions and suggest that more work should be done on this link.
Quality Management in Small and Medium Sized Enterprises

Traditionally, the main focus of research of Quality Management has been on larger organizations. While these are important, so are the SMEs which are crucial to the national economy. However, there is no larger adoption of improvement processes in these smaller companies, even though studies suggest that Quality Management is implementable in smaller companies as well as in larger ones. Due to differences in characteristics, such as available resources, between SMEs and larger organizations, there seems to be a need for distinct treatment of SMEs. This paper reviews literature on QM implementation in SMEs. It synthesizes advices into six main categories: Involve external support, Involve employees, Implement gradually with realistic goals, Involve management, Track performance and benchmark, and Contextualize to the organization. The paper discusses the need for individual approaches for each SME when designing an improvement program, as well as the feasibility of a general approach when compared to larger organisations.
Partner Disclosure : An Examination of Investor Reaction to Negative Information and Potential Implications for Auditor Independence

The PCAOB recently issued two successive concept releases which seek feedback on a proposed amendment that would require audit partner name disclosure (“partner disclosure”) in the standard current year audit report (PCAOB 2008; PCAOB 2009; PCAOB 2011). The motivation behind the potential new requirement is to increase accountability on the part of the audit partner and transparency for interested parties who rely upon the financial statements (ACAP 2008; PCAOB 2008; PCAOB 2009; PCAOB 2011). We develop a model to explore the potential effect of a partner disclosure requirement on auditor independence. Specifically, we contend that partner disclosure may lead to an unintended transfer of (potentially biased) information from one reporting entity to another. We outline how this information transfer might alter audit partners’ incentive structures as they seek to minimize their personal reputational costs. We further explain how this might align partner incentives more closely with those of management, potentially resulting in impaired audit independence. We collect and present experimental evidence to substantiate this potential for audit information transfer (i.e., the first link in our model). We find that investors, particularly those with less experience working with financial statements, are less likely to invest in a reporting entity linked to a restating peer firm via the same audit partner than when the identity of the engagement partner is not disclosed (and the link is through the same audit firm/office only). In additional analyses, we show that this effect is partially mediated by our participants’ assessed likelihood that the linked firm will experience a restatement in the future.
Parent‐reported symptoms of hyperactivity and attention deficits predict teacher‐reported symptoms

The object of the study was to examine whether symptoms of attention problems and hyperactivity reported by parents predicted teacher‐reported symptoms in a referred sample of boys with the DSM‐III‐R diagnosis of Attention‐deficit Hyperactivity Disorder (ADHD). Data from 48 boys, 7–12 years, were gathered independently from parents and teachers using the Child Behavior Checklist, Teacher's Report Form and the ADHD Rating Scale. Base rate, positive predictive power and negative predictive power were calculated for each symptom and for clusters of symptoms. The positive predictive power for individual symptoms was reasonably high with a mean score of 80%, while the parent‐teacher agreement (measured by phi correlations) was low. Our results indicate that in most children referred because of hyperactivity, inattention and impulsivity, parent reports are sufficient to make a diagnostic evaluation. However, when multiple informants are available, data should be obtained from different sources.
The biology of SPARC, a protein that modulates cell‐matrix interactions

An extracellular matrix‐associated glycoprotein expressed in a variety of tissues during embryo‐genesis and repair, SPARC contains modular domains that can function independently to bind cells and matrix components. Because SPARC can selectively disrupt cellular contacts with matrix and thereby effect changes in cell shape, it has been referred to as an antiadhesin. Inhibition of the expression of SPARC altered axial development in frogs, and deregulated expression in nematode worms resulted in a derangement of muscle attachment and embryonic lethality. SPARC also inhibits cell cycle progression in vitro, in part through a cationic, disulfide‐bonded region that is homologous to a repeated domain in the cytokine inhibitor, follistatin. Moreover, SPARC binds specifically to the B chain of platelet‐derived growth factor and alters the response of cells to several cytokines. Although information concerning the expression, biochemical properties, and cellular activities of SPARC has increased significantly over the last decade, the precise function of the protein has not been resolved. Goals of future studies include characterization of cell‐surface receptors for SPARC and the interactions with morphogens and growth factors that regulate specific activities during animal development. —Lane, T. F. , Sage, E. H. The biology of SPARC, a protein that modulates cell‐matrix interactions. FASEB J. 8: 163‐173; 1994.
Genetic and environmental influences on infant weight and weight change: The Fels longitudinal study

Despite significant progress in understanding the mechanisms by which the prenatal/maternal environment can alter development and adult health, genetic influences on normal variation in growth are little understood. This work examines genetic and nongenetic contributions to body weight and weight change during infancy and the relationships between weight change and adult body composition. The dataset included 501 white infants in 164 nuclear and extended families in the Fels Longitudinal Study, each with 10 serial measures of weight from birth to age 3 years and 232 with body composition data in mid‐adulthood. Heritability and covariate effects on weight and weight z‐score change from birth to 2 years of age were estimated using a maximum likelihood variance decomposition method. Additive genetic effects explained a high proportion of the variance in infant weight status (h2 = 0.61–0.95), and change in weight z‐score (h2 = 0.56–0.82). Covariate effects explained 27% of the phenotypic variance at 0–1 month of age and declined in effect to 6.9% of phenotypic variance by 36 months. Significant sex, gestational age, birth order, birth year, and maternal body mass index effects were also identified. For both sexes, a significant increase in weight z‐score (≫2 SD units) (upward centile crossing) was associated with greater adulthood stature, fat mass, and percent body fat than decrease or stability in weight z‐score. Understanding genetic influences on growth rate in a well‐nourished, nutritionally stable population may help us interpret the causes and consequences of centile crossing in nutritionally compromised contexts. Am. J. Hum. Biol., 2007. © 2007 Wiley‐Liss, Inc.
Are Reemployment Services Effective? Experimental Evidence from the Great Recession

We report the results of a random assignment study of a reemployment program implemented in the United States during the Great Recession which required Unemployment Insurance (UI) recipients to undergo an eligibility review and receive comprehensive job-counseling services. The program expedited participant exit from UI, produced substantial UI savings, and improved participant employment rates and earnings. These effects are associated with: (1) increased participant UI exit up to the time of services receipt, indicating an effect due to participant efforts to avoid program activities or failure to meet UI eligibility requirements; and (2) greater exit subsequent to services receipt, implying that the services themselves helped participants conduct an effective job search. Our findings provide compelling evidence that reemployment programs can be effective during recessions.
On graphical tests for proportionality of hazards in two samples

In this paper, we present a class of graphical tests of the proportional hazards hypothesis for two‐sample censored survival data. The proposed tests are improvements over some existing tests based on asymptotic confidence bands of certain functions of the estimated cumulative hazard functions. The new methods are based on the comparison of unrestricted estimates of the said functions and their restricted versions under the hypothesis. They combine the rigour of analytical tests with the descriptive value of plots. Monte Carlo simulations suggest that the proposed asymptotic procedures have reasonable small sample properties. The power is much higher than existing graphical tests and comparable with existing analytical tests. The method is then illustrated through the analysis of a data set on bone marrow transplantation for Leukemia patients. Copyright © 2015 John Wiley & Sons, Ltd.
Nutrient effects on ovulation rate, ovarian function and the secretion of gonadotrophic and metabolic hormones in sheep.

Nutrition is one of the most significant influences on the ovulation rate of sheep. In the extensive systems of husbandry practised in many countries most animals will experience at least one period of nutritional deprivation during their lifetime. Under these conditions reproductive performance is often sub-optimal, an effect usually attributed to poor nutrition. The effects of poor nutrition on reproductive performance are evident in many events in the reproductive cycle and the one which this paper will highlight is ovulation.