Miracle-dz/UniFAR-FTUs huggingface dataset:
Activation of the hedgehog signaling pathway in the developing lens stimulates ectopic FoxE3 expression and disruption in fiber cell differentiation.

PURPOSE The signaling pathways and transcriptional effectors responsible for directing mammalian lens development provide key regulatory molecules that can inform our understanding of human eye defects. The hedgehog genes encode extracellular signaling proteins responsible for patterning and tissue formation during embryogenesis. Signal transduction of this pathway is mediated through activation of the transmembrane proteins smoothened and patched, stimulating downstream signaling resulting in the activation or repression of hedgehog target genes. Hedgehog signaling is implicated in eye development, and defects in hedgehog signaling components have been shown to result in defects of the retina, iris, and lens. METHODS We assessed the consequences of constitutive hedgehog signaling in the developing mouse lens using Cre-LoxP technology to express the conditional M2 smoothened allele in the embryonic head and lens ectoderm. RESULTS Although initial lens development appeared normal, morphological defects were apparent by E12.5 and became more significant at later stages of embryogenesis. Altered lens morphology correlated with ectopic expression of FoxE3, which encodes a critical gene required for human and mouse lens development. Later, inappropriate expression of the epithelial marker Pax6, and as well as fiber cell markers c-maf and Prox1 also occurred, indicating a failure of appropriate lens fiber cell differentiation accompanied by altered lens cell proliferation and cell death. CONCLUSIONS Our findings demonstrate that the ectopic activation of downstream effectors of the hedgehog signaling pathway in the mouse lens disrupts normal fiber cell differentiation by a mechanism consistent with a sustained epithelial cellular developmental program driven by FoxE3.
Changes in lipid profile observed in children over the course of infectious disease

Lipid profile was evaluated prospectively in 23 consecutive children, aged 3.2–14.9 years, admitted to the hospital with a febrile illness (pneumonia, upper respiratory tract infection, diarrhea, pyelonephritis, mononucleosis, appendicitis). The degree of dyslipidemia associated with fever was assessed using each child as his/her own control and by comparison with 93 non‐febrile children who had no evidence of fever during the past six months. Total cholesterol decreased during the symptomatic phase of the disease. The magnitude and duration of its decrease appeared to be related to the degree and duration of fever. Low HDL‐cholesterol and hypertriglyceridemia were observed during the late stage of the febrile disease and were still detected in the convalescent phase. This study suggests that in children, transient and sometimes prolonged lipid changes may occur in association with an infectious febrile disease. This effect is important for defining the appropriate timing for screening for dyslipidemias.
Nucleotide and deduced amino acid sequences of the lacR, lacABCD, and lacFE genes encoding the repressor, tagatose 6-phosphate gene cluster, and sugar-specific phosphotransferase system components of the lactose operon of Streptococcus mutans

The complete nucleotide sequences of lacRABCDF and partial nucleotide sequence of lacE from the lactose operon of Streptococcus mutans are presented. Comparison of the streptococcal lac determinants with those of Staphylococcus aureus and Lactococcus lactis indicate exceptional protein and nucleotide identity. The deduced polypeptides also demonstrate significant, but lower, sequence similarity with the corresponding lactose proteins of Lactobacillus casei. Additionally, LacR has sequence homology with the repressor (DeoR) of the Escherichia coli deoxyribonucleotide operon, while LacC is similar to phosphokinases (FruK and PfkB) from E. coli. The primary translation products of the lacRABCDFE genes are polypeptides of 251 (M(r) 28,713), 142 (M(r) 15,610), 171 (M(r) 18,950), 310 (M(r) 33,368), 325 (M(r) 36,495), 104 (M(r) 11,401), and 123 (NH2-terminal) amino acids, respectively. As inferred from their direct homology to the staphylococcal lac genes, these determinants would encode the repressor of the streptococcal lactose operon (LacR), galactose-6-phosphate isomerase (LacA and LacB), tagatose-6-phosphate kinase (LacC), tagatose-1,6-bisphosphate aldolase (LacD), and the sugar-specific components enzyme III-lactose (LacF) and enzyme II-lactose (LacE) of the S. mutans phosphoenolpyruvate-dependent phosphotransferase system. The nucleotide sequence encompassing the S. mutans lac promoter appears to contain repeat elements analogous to those of S. aureus, suggesting that repression and catabolite repression of the lactose operons may be similar in these organisms.
The CEO's Attitude Towards the Shareholder Value and the Stakeholder Model. A Comparison Between the Continental European and the Anglo-Saxon Perspective

The debate on shareholder value versus stakeholder orientation is more than ever an issue, particularly, since the burst of the internet bubble and corporate scandals in the United States have scrutinized prevalent management practices. There are also some arguments that the shareholder model will prevail due to the globalization of capital markets and the growing power of institutional investors. This paper addresses the issue of shareholder value versus stakeholder orientation in firms. It provides new evidence of CEOs’ preferred orientation across countries. The findings of our study indicate that American and British CEOs favor maximizing shareholder value and European CEOs focus on engaging with the stakeholders. In addition a case study of Shell in the 1990s is presented indicating that firms are able to achieve outstanding returns for their shareholders in the long run not despite but because of their stakeholder orientation.
Influence Fields : A Quantitative Framework for the Representation and 1 Analysis of Active Dendrites 2

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India. 4 5 Corresponding Author 6 7 Rishikesh Narayanan, Ph.D. 8 Molecular Biophysics Unit 9 Indian Institute of Science 10 Bangalore 560 012, India. 11 12 e-mail: rishi@mbu.iisc. ernet.in 13 Phone: +91-80-22933372 14 Fax: +91-80-23600535 15 16 17 18 19 Abbreviated title: Quantifying active dendrites using influence fields 20 21 Number of words in abstract: 249 22 Number of figures: 10 23 Number of tables: 2 24 25
CyberparaBLAST: the parallelized BLAST Web server

Retrieving homologous sequences from existing databases, for instance, is a fundamental routine for the bioinformatics research community. Programs of the NCBI BLAST family have been widely used for retrieving homologous sequences from existing databases. This article briefly introduces and evaluates a parallelized version of the BLAST algorithm using Message Passing Interface (MPI) on a multi-node compute cluster, paraBLAST and its Web server, CyberparaBLAST. The CyberparaBLAST Web server can be accessed through Web browsers on intranet Web servers. CyberparaBLAST enables the researchers of institutes to query sequence databases in the real time when needed. Parallelized computing together with cyber access make the bioinformatics research more efficient with the aid of CyberparaBLAST.
Culture-Independence for Surveillance and Epidemiology

Culture-independent methods in microbiology (quantitative PCR (qPCR), sequencing, microarrays, direct from sample matrix assisted laser desorption/ionization time of flight mass spectroscopy (MALDI-TOF MS), etc.) are disruptive technology. Rather than providing the same results as culture-based methods more quickly, more cheaply or with improved accuracy, they reveal an unexpected diversity of microbes and illuminate dark corners of undiagnosed disease. At times, they overturn existing definitions of presumably well-understood infections, generating new requirements for clinical diagnosis, surveillance and epidemiology. However, current diagnostic microbiology, infection control and epidemiology rest principally on culture methods elegantly optimized by clinical laboratorians. The clinical significance is interwoven; the new methods are out of context, difficult to interpret and impossible to act upon. Culture-independent diagnostics and surveillance methods will not be deployed unless the reported results can be used to select specific therapeutics or infection control measures. To cut the knots surrounding the adoption of culture-independent methods in medical microbiology, culture-dependent methods should be supported by consistent culture-independent methods providing the microbial context. This will temper existing biases and motivate appropriate scrutiny of the older methods and results.
Recent advances on TD-SCDMA in China

China has fully embraced the remarkable growth and unprecedented penetration of mobile services, and has become the world's largest mobile cellular market. TD-SCDMA was proposed by the China Wireless Technology Standard (CWTS) Group in 1998, approved as one of the 3G standards by ITU in May 2000, and joined 3GPP in March 2001. This has been a major effort by China to advance its mobile communication systems and facilitate its own technological development in this critical area. TD-SCDMA, a combination of TDD and synchronous CDMA, offers several unique advantages over its alternatives, WCDMA and cdma2000, such as flexible spectrum allocation, low-cost implementation, and easier migration from GSM systems. This article reviews the development, key technical features, and deployment of TD-SCDMA in China.
Stratospheric Harbingers of Anomalous Weather Regimes

Observations show that large variations in the strength of the stratospheric circulation, appearing first above ∼50 kilometers, descend to the lowermost stratosphere and are followed by anomalous tropospheric weather regimes. During the 60 days after the onset of these events, average surface pressure maps resemble closely the Arctic Oscillation pattern. These stratospheric events also precede shifts in the probability distributions of extreme values of the Arctic and North Atlantic Oscillations, the location of storm tracks, and the local likelihood of mid-latitude storms. Our observations suggest that these stratospheric harbingers may be used as a predictor of tropospheric weather regimes.
Ciliary muscle capillaries have blood-tissue barrier characteristics.

It was determined whether the capillaries in the ciliary muscle are of the blood-tissue barrier or of the permeable non-barrier type. Ciliary body and iris of normal human and animal eyes were examined by electron microscopy and by immunohistochemical staining with a panel of antibodies recognizing endothelial blood-brain barrier markers. In addition, horseradish peroxidase (HRP) tracer studies of the anterior segment were carried out in rabbits. Our results demonstrated that the capillary endothelium in human and rabbit ciliary muscle has few luminal pinocytotic vesicles and a morphological aspect suggesting the presence of tight junctions. Ciliary muscle and iris capillaries stained positive for the blood-brain barrier markers Glucose-Transporter-1 and P-Glycoprotein, while staining for the PAL-E antigen and the transferrin receptor was absent. In the rabbit ciliary muscle, vascular leakage of exogenous HRP tracer was absent. It was concluded that this functional barrier and the observed phenotype of ciliary muscle capillaries are consistent with a blood-tissue barrier function similar to that of the iris microvasculature.
Nerve Growth Factor-induced Neuronal Differentiation Requires Generation of Rac1-regulated Reactive Oxygen Species*

Nerve growth factor (NGF) stimulation of pheochromocytoma PC12 cells transiently increased the intracellular concentration of reactive oxygen species (ROS). This increase was blocked by the chemical antioxidant N-acetylcysteine and a flavoprotein inhibitor, diphenylene iodonium. NGF responses of PC12 cells, including neurite outgrowth, tyrosine phosphorylation, and AP-1 activation, was inhibited when ROS production was prevented byN-acetylcysteine and diphenylene iodonium. The expression of dominant negative Rac1N17 blocked induction of both ROS generation and morphological differentiation by NGF. The ROS produced appears to be H2O2, because the introduction of catalase into the cells abolished NGF-induced neurite outgrowth, ROS production, and tyrosine phosphorylation. These results suggest that the ROS, perhaps H2O2, acts as an intracellular signal mediator for NGF-induced neuronal differentiation and that NGF-stimulated ROS production is regulated by Rac1 and a flavoprotein-binding protein similar to the phagocytic NADPH oxidase.
Chest Physiotherapy Techniques Used in Neonatal & Paediatric Intensive Care Units in Punjab

The purpose of this study was to observe the common chest physiotherapy techniques (CPT) used by physiotherapists in Neonatal and Paediatric Intensive Care Units (NICU &PICU) in the hospitals located in Punjab. The design of the study was exploratory cross sectional survey. Data was collected with the help of standardised questionnaire, which was sent to one hundred thirty therapists who worked in thirty eight different hospitals in Punjab and these hospitals have claimed physiotherapy facilities in their NICU and PICU premises. A period of two weeks was given to the therapists for the completion of questionnaire. If the therapists were not able to send the filled questionnaire within two weeks, then a reminder call was given to them for the next two consecutive weeks. It was found that only eighty-four (i.e. 64.61%) completed questionnaires was received from the twenty five hospitals. It was concluded that percussion, vibration, suctioning, positioning, breathing exercises of CPT techniques were commonly practised in both PICU and NICU.
[The neurobehavioral rating scale-revised: assessment of concurrent validity].

UNLABELLED Cognitive and behavioral impairment are a major source of disability in daily living of patients with traumatic brain injury (TBI). The Neurobehavioral Rating Scale-Revised (NRS-R) is a short, easy-to administer interview tool developed to improve assessment by clinicians. Data are available on its criterion validity and reliability, but the concurrent validity of the French NRS-R was not yet documented. OBJECTIVE To assess the concurrent validity of the NRS-R with current psychometric tests. METHOD One hundred and four patients with TBI enrolled in a community adjustment program underwent concurrent examination with the NRS-R, cognitive tests assessing memory, attention, and executive functions, and scales of anxiety (STAI) and depressive mood (CES-D). Intercorrelations were undertaken between these variables and the five factors of the NRS-R: F1, intentional behavior; F2, lowered emotional state; F3, survival-oriented behaviour/hightened emotional state; F4, arousal state; and F5, language. Patients were 82 men and 22 women, the mean age was 28.5 years, and 70% had severe TBI (Glasgow coma score [GCS] below 8 on admission). They were assessed 52 months on average after their injury. RESULTS Factor F1 was correlated with results on the GCS (P<0.05), the Tower of London test (TL, P<0.01), the Trail Making Test (TMT, P<0.01), divided attention (DA) and inhibition (IN) subscales of the Zimmermann and Fimm's Attention battery (TEA) (P<0.01) and reverse digit span (DS, P<0.05). Factor F2 was positively related to age at injury, time since injury (TSI) (P<0.05) and CESD and STAI scores (P<0.001). Factor F3 was related to DA (P<0.01) TL scores and TSI (P<0.05). Factor F4 was related to TL, TMT, DA, flexibility, DS (P<0.05), TSI, duration of post-traumatic amnesia, CES-D score (P<0.05) and STAI scores (P<0.01). Factor F5 was related to GCS, DA (P<0.05), and reaction time on the subscales IN and Go/nogo (GO) of the TEA battery (P<0.01). The NRS-R total score was related to CESD, STAI scores, TMT score, DA (P<0.01) and TL score, IN and GO scores and TSI (P<0.05). DISCUSSION As McCauley et al found with the English version of the NRS-R, significant relationships were found between NRS-R factor scores, cognitive tests and emotional scales. Relationships were also found between factor scores and indicators of injury severity and time since injury. These data suggest fair concurrent validity of the NRS-R.
The long‐range electrostatic interactions control tRNA–aminoacyl‐tRNA synthetase complex formation

In most cases aminoacyl‐tRNA synthetases (aaRSs) are negatively charged, as are the tRNA substrates. It is apparent that there are driving forces that provide a long‐range attraction between like charge aaRS and tRNA, and ensure formation of “close encounters. ” Based on numerical solutions to the nonlinear Poisson‐Boltzmann equation, we evaluated the electrostatic potential generated by different aaRSs. The 3D‐isopotential surfaces calculated for different aaRSs at 0.01 kT/e contour level reveal the presence of large positive patches—one patch for each tRNA molecule. This is true for classes I and II monomers, dimers, and heterotetramers. The potential maps keep their characteristic features over a wide range of contour levels. The results suggest that nonspecific electrostatic interactions are the driving forces of primary stickiness of aaRSs–tRNA complexes. The long‐range attraction in aaRS–tRNA systems is explained by capture of negatively charged tRNA into “blue space area” of the positive potential generated by aaRSs. Localization of tRNA in this area is a prerequisite for overcoming the barrier of Brownian motion.
Continuous Integration: The Silver Bullet?

Continuous integration (CI) tools integrate code changes by automatically compiling, building, and executing test cases upon submission of code changes. Use of CI tools is getting increasingly popular, yet how proprietary projects reap the benefits of CI remains unknown. To investigate the influence of CI on software development, we mine 661 open source software (OSS) projects, and 171 proprietary projects. For OSS projects, we observe the expected benefits after CI adoption, i.e. more bugs are resolved, and more issues are resolved. However, for the proprietary projects, we cannot make similar observations. Therefore, we cannot claim that CI is the `silver bullet' for software development. Why is this so? Our findings indicate that only adoption of CI might not be enough to improve software development. CI can be effective for software development if practitioners use CI's feedback mechanism efficiently, by applying the practice of making frequent commits. For proprietary projects we observe practitioners to commit less frequently, and hence not use CI effectively, for obtaining feedback on the submitted code changes. We recommend practitioners to (i) apply the CI best practices along with adoption of CI tools, (ii) consider their team's development context before adopting CI tools, and (iii) after adoption of CI, investigate if CI satisfies their needs by applying software analytics.
Cross-Weighted Moments and Affine Invariants for Image Registration and Matching

A framework for deriving a class of new global affine invariants for both object matching and positioning based on a novel concept of cross-weighted moments with fractional weights is presented. The fractional weight factor allows for a more flexible range to balance between the capability to discriminate between objects that differ only in small shape details and the sensitivity of small shape details to the presence of the noise. Moreover, it makes it possible to arrive at low order (zero order) affine invariants that are more robust than those derived from higher order regular moments. The affine transformation parameters are recovered from the zero and the first order cross-weighted moments without requiring any feature point correspondence information. The equations used to find the affine transformation parameters are linear algebraic. The sensitivity of the cross-weighted moment invariants to noise, missing data, and perspective effects is shown on real images.
Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.

A nitrogen-fixing bacterium, designated NF2-4-5T, was isolated from a paddy soil in Anseong City, Korea. Cells of strain NF2-4-5T were Gram-staining-positive, motile rods and aerobic. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus and was closely related to Paenibacillus graminis RSA19T (98.7 %), Paenibacillus jilunlii Be17T (98.6 %), Paenibacillus salinicaeni LAM0A28T (98.6 %) and Paenibacillus riograndensis SBR5T (98.6 %). Growth of strain NF2-4-5T occurs at temperatures of 18-37 °C, at pH 6.0-8.5 and between 0.5% and 2 % NaCl (w/v). The only respiratory quinone was MK-7. The cell wall peptidoglycan of strain NF2-4-5T contained meso-diaminopimelic acid. The main cellular fatty acids were C16 : 0 and anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The DNA G+C content was 56.36 mol%. The DNA-DNA hybridization relatedness between strain NF2-4-5T and four reference strains, Paenibacillus graminis RSA19T, Paenibacillus jilunlii Be17T, Paenibacillus sonchi X19-5T and Paenibacillus riograndensis SBR5T, was 22.0±0.3, 20.1±0.7, 18.3±0.3 and 12.6±0.5 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that the strain NF2-4-5T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus azotifigens sp. nov. is proposed. The type strain is NF2-4-5T (=KACC 18967T=LMG 29963T).
A facile synthesis and photoluminescence properties of water-dispersible Re3+ doped CeF3 nanocrystals and solid nanocomposites with polymers.

Water-dispersible Re(3+) doped CeF(3) colloidal nanocrystals with well controllable morphology and high crystallinity have been successfully synthesized through a solvothermal process. The TEM images illustrate that the Re(3+) doped CeF(3) nanocrystals are rectangular (or cubic) with a mean diameter of ~10 nm. The excellent dispersibility in some of the polar solvents including water is achieved by using polyethyleneimine as the capping agent. The amine groups of the polymer chains on one hand bind to the nanocrystal surface; on the other hand the free ones could link to functional materials including bio-molecules. The CeF(3) nanocrystals doped with Tb(3+) and Dy(3+) ions show the characteristic emission of Tb(3+ 5)D(4)-(7)F(J) (J = 6-3, with (5)D(4)-(7)F(5) green emission at 542 nm as the strongest one) and Dy(3+ 4)F(9/2)-(6)H(15/2) (blue-green color at 478 nm) and (4)F(9/2)-(6)H(13/2) (yellow color at 571 nm) transitions, respectively. The energy transfer from Ce(3+) to Tb(3+) and Dy(3+) was also investigated in detail. In vitro studies of Re(3+) doped CeF(3) colloidal nanocrystals on HepG2 cells confirm their excellent biological compatibility. The obtained solid CeF(3) : Tb(3+)/PDMS nanocomposites are very stable and flexible and exhibit strong green photoluminescence upon UV excitation.
An endoplasmic reticulum-specific cyclophilin

Cyclophilin is a ubiquitously expressed cytosolic peptidyl-prolyl cis-trans isomerase that is inhibited by the immunosuppressive drug cyclosporin A. A degenerate oligonucleotide based on a conserved cyclophilin sequence was used to isolate cDNA clones representing a ubiquitously expressed mRNA from mice and humans. This mRNA encodes a novel 20-kDa protein, CPH2, that shares 64% sequence identity with cyclophilin. Bacterially expressed CPH2 binds cyclosporin A and is a cyclosporin A-inhibitable peptidyl-prolyl cis-trans isomerase. Cell fractionation of rat liver followed by Western blot (immunoblot) analysis indicated that CPH2 is not cytosolic but rather is located exclusively in the endoplasmic reticulum. These results suggest that cyclosporin A mediates its effect on cells through more than one cyclophilin and that cyclosporin A-induced misfolding of T-cell membrane proteins normally mediated by CPH2 plays a role in immunosuppression.