Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementary Material : Geometric Descent Method for Convex Composite Minimization

We argue that the geometric intuition of GeoPG is still clear. Note that we are still constructing two balls that contain x∗ and shrink at the same absolute amount. In GeoPG, since we assume that the smooth function f is strongly convex, we naturally have one ball that contains x∗, and this ball is related to the proximal gradient Gt, instead of the gradient due to the presence of the nonsmooth function h. To construct the other ball, GeoD needs to perform an exact line search, while our GeoPG needs to find the root of a newly constructed function φ̄, which is again due to the presence of the nonsmooth function h. The two changes of GeoPG from GeoD are: replace gradient by proximal gradient; replace the exact line search by finding the root of φ̄, both of which are resulted by the presence of the nonsmooth function h.
Impact of Venous-Systemic Oxygen Persufflation With Nitric Oxide Gas on Steatotic Grafts After Partial Orthotopic Liver Transplantation in Rats

Background Steatotic livers are associated with poor graft function after transplantation. We investigated the effects of venous-systemic oxygen persufflation with nitric oxide gas (VSOP-NO) on steatotic partial livers after transplantation. Methods Steatotic livers induced by fasting for 2 days and subsequent refeeding for 3 days with a fat-free, carbohydrate-rich diet were reduced in size by 50% and transplanted into Lewis rats after 3 hr of cold storage in histidine-tryptophan-ketoglutarate solution. Gaseous oxygen with nitric oxide (40 ppm) was insufflated into the grafts through the suprahepatic vena cava during cold storage (VSOP-NO group; n=20). Transplantation of cold-static stored steatotic and normal grafts served as controls (Steatotic-Control and Normal-Control, respectively; n=20 for each group). Results The graft microcirculation and portal venous flow were increased by VSOP-NO compared with Steatotic-Control (P<0.001 for both). Serum alanine aminotransferase and interleukin-6 levels were lower in VSOP-NO versus Steatotic-Control group (P=0.03 for both). Messenger RNA expression for inducible nitric oxide synthase, which was increased in Steatotic-Control livers 3 hr after transplantation (P=0.02 vs. that at 1 hr), was suppressed by VSOP-NO. Although serum nitrite levels were decreased 1 hr after transplantation in Steatotic-Control (P=0.06 vs. Normal-Control), the VSOP-NO group showed increased levels comparable to Normal-Control. In livers 24 hr after transplantation, moderate vacuolization of hepatocytes by histology with the immunohistochemical expression of nitrotyrosine, indicative of nitrative stress, was found in Steatotic-Control, whereas these findings were less apparent in VSOP-NO–treated livers. Conclusions Application of VSOP-NO for steatotic partial livers reduces hepatocellular damage and improves graft viability and microcirculation after transplantation.
Photoreactions of Tyr8- and Gln50-mutated BLUF domains of the PixD protein of Thermosynechococcus elongatus BP-1: photoconversion at low temperature without Tyr8.

We studied the photoreaction of a blue-light sensor PixD protein of Thermosynechococcus elongatus that has the blue-light-using flavin (BLUF) domain. The Tyr8 and Gln50 residues of the protein were modified to phenylalanine, alanine, or asparagine (Y8F, Y8A, Q50N, and Q50A) by site-directed mutagenesis. The following results were obtained. (1) At room temperature, blue-light illumination induced the red shift of the absorption bands of flavin in the wild-type (WT) protein but not in the Y8F, Y8A, Q50A, and Q50N mutant proteins, as reported [Okajima, K. , et al. (2006) J. Mol. Biol. 363, 10-18]. (2) At 80 K, neither the Q50N nor the Q50A mutant protein accumulated the red-shifted form. (3) At 80 K, the Y8F protein photoaccumulated the red-shifted forms to an extent that was half that in the WT protein at a 43-fold slower rate, and the Y8A protein to the one-fourth the extent at a 137-fold slower rate. (4) The red-shifted form in the Y8F protein was stable below 240 K and became unstable above 240 K in the dark. (5) The illumination of the Y8F protein at 150 K accumulated the red-shifted form at the beginning, and the prolonged illumination accumulated the flavin anions by the secondary photoreaction. (6) The results indicate that Tyr8 is not indispensable for the accumulation of the red-shifted form at least at 80 K. (7) Photoconversion mechanisms in the WT and Tyr8-mutated proteins are discussed in relation to the schemes with and without the electron transfer between Tyr8 and flavin in the first step of the photoconversion.
First reported detection of a low pathogenicity avian influenza virus subtype H9 infection in domestic fowl in England

In December 2010, infection with a H9N1 low pathogenicity avian influenza (LPAI) virus was detected in a broiler breeder flock in East Anglia. Disease suspicion was based on acute drops in egg production in two of four sheds on the premises, poor egg shell quality and evidence of diarrhoea. H9N1 LPAI virus infection was confirmed by real-time reverse transcription PCR. Sequencing revealed high nucleotide identity of 93.6 per cent and 97.9 per cent with contemporary North American H9 and Eurasian N1 genes, respectively. Attempted virus isolation in embryonated specific pathogen free (SPF) fowls' eggs was unsuccessful. Epidemiological investigations were conducted to identify the source of infection and any onward spread. These concluded that infection was restricted to the affected premises, and no contacts or movements of poultry, people or fomites could be attributed as the source of infection. However, the infection followed a period of extremely cold weather and snow which impacted on the biosecurity protocols on site, and also led to increased wild bird activity locally, including waterfowl and game birds around the farm buildings. Analysis of the N1 gene sequence suggested direct introduction from wild birds. Although H9 infection in poultry is not notifiable, H9N2 LPAI viruses have been associated with production and mortality episodes in poultry in many parts of Asia and the Middle East. In the present H9N1 outbreak, clinical signs were relatively mild in the poultry with no mortality, transient impact on egg production and no indication of zoonotic spread. However, this first reported detection of H9 LPAI virus in chickens in England was also the first H9 UK poultry case for 40 years, and vindicates the need for continued vigilance and surveillance of avian influenza viruses in poultry populations.
A Low-Affinity Serum Response Element Allows Other Transcription Factors To Activate Inducible Gene Expression in Cardiac Myocytes

ABSTRACT Hypertrophic growth of cardiac muscle cells is induced by a variety of physiological and pathological stimuli and is associated with a number of changes, including activation of genes such as atrial natriuretic factor. We found that two serum response element (SRE)-like DNA elements, one of which does not meet the consensus sequence and binds serum response factor (SRF) with low affinity, regulate the activity of this promoter. Surprisingly, the ability to induce the promoter by two different physiologic stimuli, as well as various activated transcription factors, including SRF-VP16, was primarily dependent upon the nonconsensus rather than the consensus SRE. This SRE controls the induction of gene expression via an unusual mechanism in that it is required to allow some, but not all, active transcription factors at unrelated sites on the promoter to stimulate gene expression. Thus, in addition to regulation of SRF activity by growth stimuli, regulation of a low-affinity SRE element controls inducible gene expression by modulating the ability of other transcription factors to stimulate the transcription machinery.
Influence of morphology and drug distribution on the release process of FITC-dextran-loaded microspheres prepared with different types of PLGA

The aim of the present work was to understand the collaborative roles and the comprehensive effects of polymer nature, morphology, drug distribution and release behaviour for PLGA microspheres prepared by the double emulsion method. The morphology and drug distribution of the FITC-dextran-loaded microspheres were investigated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM), respectively. The results show that the morphology and release profiles depend on the polymer nature. For the capped PLGA RG502, the porosity, pore size and drug distribution had no pronounced influence on the release profile beyond the initial release. No significant changes in size and morphology were found and there was negligible water uptake during the release process. PEG addition as a pore maker indicated a possible way to modify the release rate at the second release stage. However, in the case of the uncapped PLGA RG503H, release profiles were dependent upon changes in porosity, pore size and drug loading. Increases in porosity, internal pore size and loading resulted in a continuous release profile. Previous studies have shown the importance of different process parameters on morphology and drug release, but in this work it is clear that polymer nature is a determining factor.
Optimization of requantization parameter for MPEG transcoding

This paper considers transcoding in which an MPEG stream is converted to a low-bit-rate MPEG stream, and proposes a method in which the transcoding error can be reduced by optimally selecting the quantization parameter for each macroblock. In transcoding with a low compression ratio, it is crucial to prohibit transcoding with a requantization parameter which is 1 to 2 times the quantization parameter of the input stream. Consequently, as the first step, an optimization method for the requantization parameter is proposed which cares for the error propagation effect by interframe prediction. Then, the proposed optimization method is extended so that the method can also be applied to the case of a high compression ratio in which the rate—distortion curve is approximated for each macroblock in the range of requantization parameters larger than 2 times the quantization parameter. It is verified by a simulation experiment that the PSNR is improved by 0.5 to 0.8 dB compared to the case in which a 6 Mbit/s MPEG stream is not optimized by twofold recompression. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(9): 21–30, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10096
Pressure sensing and drag estimation for fishlike swimming in uniform flows

This paper concentrates on whether the sensed pressure on swimming body surfaces may reflect the around flow velocity. First of all, hydrodynamics of specified biomimetic fishlike swimming is computationally studied with assumptions of uniform flows. The hydrodynamic lagging effect is emphasized since the lagging value has a close relationship with around flows. The spatial distribution and time variation of pressure are analyzed as well. Furthermore, the relationship between form drag and inlet flow velocity is presented. Through the virtual pressure information collected on the fish body surface, the pressure sensors are simulated as one of the functions of fish lateral line system. The proposed principle of multi-point surface pressures against flow velocities is of significance to further promote flow sensing and control methods of fish-inspired underwater vehicles.
Microtiter Plate Assay for Assessment of Listeria monocytogenes Biofilm Formation

ABSTRACT Listeria monocytogenes has the ability to form biofilms on food-processing surfaces, potentially leading to food product contamination. The objective of this research was to standardize a polyvinyl chloride (PVC) microtiter plate assay to compare the ability of L. monocytogenes strains to form biofilms. A total of 31 coded L. monocytogenes strains were grown in defined medium (modified Welshimer's broth) at 32°C for 20 and 40 h in PVC microtiter plate wells. Biofilm formation was indirectly assessed by staining with 1% crystal violet and measuring crystal violet absorbance, using destaining solution. Cellular growth rates and final cell densities did not correlate with biofilm formation, indicating that differences in biofilm formation under the same environmental conditions were not due to growth rate differences. The mean biofilm production of lineage I strains was significantly greater than that observed for lineage II and lineage III strains. The results from the standardized microtiter plate biofilm assay were also compared to biofilm formation on PVC and stainless steel as assayed by quantitative epifluorescence microscopy. Results showed similar trends for the microscopic and microtiter plate assays, indicating that the PVC microtiter plate assay can be used as a rapid, simple method to screen for differences in biofilm production between strains or growth conditions prior to performing labor-intensive microscopic analyses.
Growing pains: Non‐adherence with the immunosuppressive regimen in adolescent transplant recipients

Abstract: One‐year graft and patient survival are better in adolescent transplant recipients (age 11–19 years) than in younger (age < 11 years) pediatric transplant recipients. However, several groups found that long‐term outcomes (> i.e. 5 year post‐transplant) in the adolescent age group are significantly worse than in younger transplant recipients.
The perfect states of Keratinomyces ajelloi Vanbreuseghem, Trichophyton terrestre Durie & Frey and Microsporum nanum Fuentes.

During investigations of soil samples from various districts in the West of Scotland using Vanbreuseghem's (1952) hair-bait method, Keratinomyces ajelloi, Trichophyton terrestre, Microsporum gypseum and Arthroderma curreyi were isolated. These fungi, and Microsporum nanum isolated from ringworm-infected pigs in Kenya, have been studied in culture on unsterilised soil. Descriptions are given of the perfect stages of K. ajelloi and M. nanum which were obtained in soil culture and that of T. terrestre which arose spontaneously in an agar slope culture. It is proposed that the perfect forms of K. ajelloi and T. terrestre be included in the genus Arthroderma Currey as A. uncinatum sp. nov. and A. quadrifidum sp. nov. respectively, and that the perfect form of M. nanum be put in the genus Nannizzia Stockdale as N. obtusa sp. nov.
Paradigmas, enfoques y métodos en la investigación educativa

En la investigacion educativa actual coexisten diversas propuestas, tendencias y metodos, los que a su vez se enmarcan en distintos paradigmas que brindan una cosmovision, de como se concibe la realidad social, que guian en gran medida el entendimiento, las acciones y decisiones que se toman en el campo de la investigacion educativa. En esta perspectiva, hoy en dia se consideran que los principales paradigmas de mayor vigencia, legitimidad y difusion son: el positivista, el naturalista y el sociocritico.
Screening of families with autosomal recessive non‐syndromic hearing impairment (ARNSHI) for mutations in GJB2 gene: Indian scenario

Several studies have reported that mutations in the GJB2 gene (coding for connexin26) are a common cause of recessive non‐syndromic hearing impairment. A GJB2 mutant allele, 35delG, has been found to have a high prevalence in most ethnic groups. Though mutations in the GJB2 gene have been shown to cause autosomal recessive deafness in Indian families, the frequencies of the various mutations are still unknown. In the present study, we analyzed 45 Indian families belonging to three different states, namely, Karnataka, Tamil Nadu, and Delhi with non‐syndromic hearing impairment and an apparently autosomal recessive mode of inheritance. All the families were initially screened for three mutations (W24X, W77X, and Q124X) by using allele‐specific PCR primers; mutations were confirmed by DNA sequencing. Families that were heterozygous or negative for tested mutations of the GJB2 gene were sequenced directly to identify the complementary mutation and other mutations in GJB2. Four families were homozygous for W24X, constituting around 8.8%. In two families, the affected individuals were compound heterozygotes for W24X; one family (DKB16) carried 35delG with W24X while the other family (DKB7) carried R143W with W24X. We suggest that W24X is a common allele among the mutations screened, causing autosomal recessive non‐syndromic hearing impairment (ARNSHI) in the Indian population. © 2003 Wiley‐Liss, Inc.
Assessment of right ventricle function and pulmonary artery circulation by cine-MRI in patients with AIDS.

OBJECTIVE To evaluate right ventricle (RV) anatomy and performance and its relationships with pulmonary circulation in AIDS patients. DESIGN We conducted a prospective blinded study by using cine-MRI, a well-accepted method to assess RV and pulmonary circulation. SETTING A university hospital. PARTICIPANTS Ten healthy volunteers and 13 asymptomatic AIDS patients. MEASUREMENTS RV end-diastolic and end-systolic volumes, RV ejection fraction (RVEF), pulmonary artery (PA) diameter, main pulmonary artery distensibility (MPAD), RV free wall diastolic thickness (RVWT), and RV mass were measured. The RVWT/left ventricular wall thickness index was calculated. RESULTS AIDS patients had significantly increased RV end-diastolic and end-systolic volumes and decreased RVEF (50 +/- 10 vs 59 +/- 6; p < 0.03). Four AIDS patients had RV wall motion abnormalities; 5 (38%) had an RVEF under 45%. RVWT, the RVWT/left ventricular wall thickness index, and PA diameter were significantly increased in AIDS patients. RV mass was increased in 54% of AIDS patients. MPAD was significantly lower in AIDS patients (18.8 +/- 15 vs 26 +/- 4; p < 0.01). A significant relationship was found between RV mass and MPAD (r = 0.76; p = 0.02). CONCLUSIONS RV function is frequently impaired in AIDS patients. Anatomic and functional abnormalities found in RV and PA parameters suggest a systolic overload on RV. Pulmonary circulation abnormalities may influence RV structure and function in AIDS patients.
A history of unemployment or sick leave influences long-term functioning and health-related quality-of-life after severe traumatic brain injury

Abstract Primary objective: The consequences of pre-morbid factors in adults with severe traumatic brain injury have not been widely addressed. This study aimed to determine whether being unemployed or on sick leave before injury influences long-term health-related quality-of-life (HRQoL) and functioning in patients with severe traumatic brain injury. Subjects: Fifty-one consecutive patients were studied; aged 16–65 years, with severe traumatic brain injury who were admitted to Sahlgrenska University Hospital, Gothenburg, from 1999–2002. Methods: The patients were assessed once, 2–11 years after trauma. Data from the time of injury were combined into a validated prognostic model to adjust for injury severity. Data on sick leave and unemployment before injury were gathered from the Swedish social insurance agency. Outcomes were measured with the Short Form-36 Health Survey, the Glasgow Outcome Scale–Extended, and a self-report questionnaire specifically designed for this study to measure functioning. Results: In a multivariate analysis, a history of sick leave/unemployment predicted a worse long-term global outcome, more problems with personal activities of daily living and worse HRQoL. Conclusion: These results should be considered when refining outcome predictions and optimizing rehabilitation interventions for patients with severe traumatic brain injury.
F-18-fluorothymidine-PET evaluation of bone marrow transplant in a rat model

ObjectiveThe success of bone marrow transplantation in hematologic and oncologic diseases depends upon the ability to provide adequate hematologic and immunologic support in a timely manner. There is no current imaging tool for the evaluation of the bone marrow compartment in the peri-transplant period. In this study, we tested our hypothesis that whole-body positron emission tomography using fluorine-18 (F-18)-fluorothymidine has the ability to provide information about the functioning normal bone marrow and its physiologic distribution. MethodsWistar Furth rats were irradiated with 950 cGy followed 2 days later by syngeneic bone marrow transplantation. The animals were subjected to positron emission tomography using F-18-fluorothymidine imaging before and after ablation as well as after 4, 7, and 14 days after bone marrow transplantation. In a different set of syngeneic bone marrow transplant model, positron emission tomography using F-18-fluorodeoxyglucose was carried out for comparison. Imaging results were correlated with marrow histology upon necropsy. ResultsF-18-fluorothymidine images showed definitive recovery of marrow within 4 days after transplant. In contrast, F-18-fluorodeoxyglucose was unable to present a corresponding picture. Sternum and humerus marrow in the images were analyzed by drawing three-dimensional regions of interest to obtain quantitative uptake value of tracers, which corroborated the image data. ConclusionWe conclude that positron emission tomography using F-18-fluorothymidine offers a clinically useful noninvasive technique to evaluate bone marrow injury and recovery.
New advances in synchronization of digital communication receivers

New Advances in Synchronization of Digital Communication Receivers. (December 2003) Yan Wang, B.S., Peking University, P.R. China; M.S., Beijing University of Posts & Telecommunications, P.R. China Chair of Advisory Committee: Dr. Erchin Serpedin Synchronization is a challenging but very important task in communications. In digital communication systems, a hierarchy of synchronization problems has to be considered: carrier synchronization, symbol timing synchronization and frame synchronization. For bandwidth efficiency and burst transmission reasons, the former two synchronization steps tend to favor non-data aided (NDA or blind) techniques, while in general, the last one is usually solved by inserting repetitively known bits or words into the data sequence and is referred to as a data-aided (DA) approach. Over the last two decades, extensive research work has been carried out to design nondata-aided timing recovery and carrier synchronization algorithms. Despite their importance and spread use, most of the existing blind synchronization algorithms are derived in an ad-hoc manner without exploiting optimally the entire available statistical information. In most cases their performance is evaluated by computer simulations; rigorous and complete performance analysis has not been performed yet. It turns out that a theoretical oriented approach is indispensable for studying the limit or bound of algorithms and for comparing different methods. The main goal of this dissertation is to develop several novel signal processing frameworks that enable one to analyze and improve the performance of the existing timing recovery and carrier synchronization algorithms. As byproducts of this analy-
Cautious NMPC with Gaussian Process Dynamics for Autonomous Miniature Race Cars

This paper presents an adaptive high performance control method for autonomous miniature race cars. Racing dynamics are notoriously hard to model from first principles, which is addressed by means of a cautious nonlinear model predictive control (NMPC) approach that learns to improve its dynamics model from data and safely increases racing performance. The approach makes use of a Gaussian Process (GP) and takes residual model uncertainty into account through a chance constrained formulation. We present a sparse GP approximation with dynamically adjusting inducing inputs, enabling a real-time implementable controller. The formulation is demonstrated in simulations, which show significant improvement with respect to both lap time and constraint satisfaction compared to an NMPC without model learning.