Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for a Mendelian gene in a segregation analysis of generalized radiographic osteoarthritis: the Framingham Study.

OBJECTIVE To investigate the inheritance of generalized osteoarthritis (OA). METHODS OA was identified on hand and knee radiographs obtained from members of the Framingham Study cohort (the parents) in 1967-1970 and 1992-1993, and from their adult children in the Framingham Offspring Study in 1993-1994. All hand and knee radiographs evaluated for OA were graded using the Kellgren and Lawrence (K/L) scale. A measure of generalized OA was defined as the count of the number of hand and knee joints affected, as determined by the proportion of joints with a K/L grade > or =2. The OA count, treated as a continuous variable, was adjusted for age, body mass index, and a measure of physical activity for each joint area (hand or knee). Calculations were made separately for each generation and each sex, and correlations were analyzed against the standardized residual of OA. Segregation analysis was used to test whether OA aggregated in families, and if its transmission fit a Mendelian pattern. RESULTS A total of 337 nuclear families with 2 parents and at least 1 biologic offspring were studied. In parents, the mean age was 61.2 years at the time of hand radiographs and 72.8 years at the time of knee radiographs, which were mostly obtained at a later examination. The mean age at the time of radiographs in offspring was 53.9 years. Using standardized residuals, parent-offspring and sibling-sibling correlations ranged from 0.115 to 0.306. In segregation analyses, models testing the hypotheses of no familial aggregation, no familial transmission, or a Mendelian gene alone were all rejected (P < 0.001 for each of these models). The best-fitting models were mixed models with a Mendelian mode of inheritance and a residual multifactorial component. The Mendelian recessive model provided the best fit. CONCLUSION These analyses support a significant genetic contribution to OA, with evidence for a major recessive gene and a multifactorial component, representing either polygenic or environmental factors.
Median nerve ultrasound as a screening tool in carpal tunnel syndrome: Correlation of cross‐sectional area measures with electrodiagnostic abnormality

Introduction: Sonographically measured median nerve cross‐sectional area (CSA) at the wrist is increased in patients with carpal tunnel syndrome (CTS). Ultrasound of the median nerve may be useful in screening for electrodiagnostic (EDx) abnormalities. Methods: EDx studies were performed on all participants. Sonographic evaluation of median nerve CSA at the wrist and in the forearm was performed by a physician blinded to the EDx results. Multivariate and receiver operating characteristic (ROC) analysis were used to assess the data. Results: Fifty control wrists and 192 symptomatic wrists were analyzed. Sensitivity of ultrasound in excluding EDx abnormality was 99% for CSA of 9 mm2 and 97% for a wrist–forearm ratio (WFR) of 1.4. There was no clinically significant correlation between ultrasound parameters and EDx severity. Conclusions: Median nerve ultrasound is a highly sensitive screening tool for EDx abnormality, but it cannot determine severity. This may lead to changes in the current standards for evaluating CTS. Muscle Nerve, 2012
The Nedd4-like Protein KIAA0439 Is a Potential Regulator of the Epithelial Sodium Channel*

The amiloride-sensitive epithelial sodium channel (ENaC) plays a critical role in fluid and electrolyte homeostasis and consists of α, β, and γ subunits. The carboxyl terminus of each ENaC subunit contains a PPxY, motif which is believed to be important for interaction with the WW domains of the ubiquitin-protein ligase, Nedd4. Disruption of this interaction, as in Liddle's syndrome, where mutations delete or alter the PPxY motif of either the β or γ subunits, has been proposed to result in increased ENaC activity. Here we present evidence that KIAA0439 protein, a close relative of Nedd4, is also a potential regulator of ENaC. We demonstrate that KIAA0439 WW domains bind all three ENaC subunits. We show that a recombinant KIAA0439 WW domain protein acts as a dominant negative mutant that can interfere with the Na+-dependent feedback inhibition of ENaC in whole-cell patch clamp experiments. We propose that KIAA0439 and Nedd4 proteins either play a redundant role in ENaC regulation or function in a tissue- and/or signal-specific manner to down-regulate ENaC.
In situ hybridization to mRNA of Arabidopsis tissue sections.

In situ hybridization detection of mRNA is an essential tool for understanding regulation of gene expression in cells and tissues of different organisms. Over the years, numerous in situ protocols have been developed ranging from whole-mount techniques that allow fast transcript localization in intact organs to high-resolution methods based on the electron microscopic detection of mRNAs at the subcellular level. Here, we present a detailed protocol for the detection of mRNAs in plant tissues using radiolabeled single-stranded RNA probes. Hybridizations are carried out on tissue sections of paraffin- and plastic-embedded plant tissues. Although this in situ protocol is appropriate for plant tissues in general, it has been optimized for Arabidopsis thaliana. Variations on the procedure, required to obtain optimal results with different Arabidopsis tissues, are described.
Early Synthesis of Budded Virus Envelope Fusion Protein GP64 Enhances Autographa californica Multicapsid Nucleopolyhedrovirus Virulence in Orally Infected Heliothis virescens

ABSTRACT Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV), the type species of the Nucleopolyhedrovirus genus (Baculoviridae family), has two highly unusual traits shared by several baculovirus species. First, the occlusion-derived virus (ODV) that establishes primary infection in the midgut following its ingestion by host larvae contains multiple nucleocapsids, all of which enter the same midgut cell. Second, GP64, the envelope fusion protein of the budded virus (BV) that spreads infection beyond the midgut, is synthesized both early and late during infection. We tested the hypothesis that, together, these two traits enable parental ODV nucleocapsids to bud from infected midgut cells, essentially as BV, to establish secondary infections prior to completion of viral replication within the midgut. This “pass-through” strategy would enable the virus to counter the host's principal defense, sloughing of infected midgut cells, by accelerating the onset of systemic infections. To test this hypothesis, we created an AcMNPV recombinant, AcLate21/20-64HB, that can express gp64 only during the late phase of infection (coincident with the other structural proteins). We then compared the virulence of this virus to that of a control recombinant virus that expresses gp64 in a wild-type manner. We found that when administered orally, the control virus was far more virulent and established secondary infection earlier than AcLate21/20-64HB, but when administered intrahemocoelically, infectivity and virulence of the two recombinants were identical. Our results demonstrate that early gp64 expression is a key component of a unique and highly adaptive baculovirus infection strategy.
Gene expression in insecticide resistant and susceptible Anopheles gambiae strains constitutively or after insecticide exposure

A microarray containing approximately 20 000 expressed sequence tags (ESTs; 11 760 unique EST clusters) from the malaria vector, Anopheles gambiae, was used to monitor differences in global gene expression in two insecticide resistant and one susceptible strains. Statistical analysis identified 77 ESTs that were differentially transcribed among the three strains. These include the cytochrome P450 CYP314A1, over‐transcribed in the DDT resistant ZAN/U strain, and many genes that belong to families not usually associated with insecticide resistance, such as peptidases, sodium/calcium exchangers and genes implicated in lipid and carbohydrate metabolism. Short‐term (6 and 10 h) effects of exposure of the pyrethroid resistant RSP strain to permethrin were also detected. Several genes belonging to enzyme families already implicated in insecticide or xenobiotic detoxification were induced, including the carboxylesterase COEAE2F gene and members of the UDP‐glucuronosyl transferase and nitrilase families.
Separation of water-nondialyzable thimerosal in serum by cysteine equilibrium dialysis.

The thimerosal content of serum assayed biologically (biological content) was markedly lower than that assayed chemically (chemical content) . About half of thimerosal added to fresh serum was changed immediately to a form nondialyzable against water; only half the chemical content possessed the preservative activity. The nondialyzable thimerosal content of fresh serum was higher than that of old serum; that of the albumin fraction higher than that of the globulin fraction. The nondialyzable thimerosal was separable by cysteine equilibrium dialysis without any loss of the antitoxin potencies . The present results indicate that only free, water-dialyzable thimerosal possesses the preservative activity and that thimerosal is not a suitable preservative for such protein -rich biological products as antitoxins, although about 50% of the added thimerosal retained the preservative activity for at least 10 months .
Virus adaptation to quantitative plant resistance: erosion or breakdown?

Adaptation of populations to new environments is frequently costly due to trade‐offs between life history traits, and consequently, parasites are expected to be locally adapted to sympatric hosts. Also, during adaptation to the host, an increase in parasite fitness could have direct consequences on its aggressiveness (i.e. the quantity of damages caused to the host by the virus). These two phenomena have been observed in the context of pathogen adaptation to host's qualitative and monogenic resistances. However, the ability of pathogens to adapt to quantitative polygenic plant resistances and the consequences of these potential adaptations on other pathogen life history traits remain to be evaluated. Potato virus Y and two pepper genotypes (one susceptible and one with quantitative resistance) were used, and experimental evolutions showed that adaptation to a quantitative resistance was possible and resulted in resistance breakdown. This adaptation was associated to a fitness cost on the susceptible cultivar, but had no consequence either in terms of aggressiveness, which could be explained by a high tolerance level, or in terms of aphid transmission efficiency. We concluded that quantitative resistances are not necessarily durable but management strategies mixing susceptible and resistant cultivars in space and/or in time should be useful to preserve their efficiency.
BILATERAL SPASTIC CEREBRAL PALSY‐MRI PATHOLOGY AND ORIGIN. ANALYSIS FROM A REPRESENTATIVE SERIES OF 56 CASES

MRI of the brain was performed on 56 children with bilateral spastic cerebral palsy (CP) at a mean age of 10.7 years. Specific pathology was found in 91 per cent; periventricular leukomalacia was present in 42 per cent of term‐ and H7 per cent of preterm‐born children. Parasagittal subeortico‐cortical injury, multicystie encephalomalacia and basal ganglia lesions were identified in 16 per cent, in all but one associated with severe peri‐/neonatal events at term or near term. Maldevelopment composed 9 per cent, all but one found in term‐born children. MRI morphology correlated strikingly with outcome. Periventricular leukomalacia was associated with more severe disability in term‐ than preterm‐born children.
Enzyme activity and seedling growth of soybean seeds under accelerated aging

Seed aging is the main problem of seed storage. Changes of bio-chemical and reduction of seedling growth are consequence of seed deterioration. An experiment was conducted to evaluate the effects of accelerated aging on soybean seed germination indexes and enzyme activity. Seeds were incubated in closed plastic boxes for the accelerated aging treatments. Three accelerate aging regimes were performed by placing seeds at 41°C and relative humidity (RH) of 90-100 % for 0, 2, 4, 6 and 8 days periods. Our results showed that increasing aging duration resulted higher reduction in germination characteristics, catalase and ascorbate peroxidase. Germination percentage, means time to germination, germination index, normal seedling percentage and enzyme activity decrease significantly.
Kalman filter approaches for a mixed clock ensemble

Clock ensembling is a promising concept for future time scale generation as robustness and stability can be considerably improved compared to master clock approaches. While ensembles consisting of the same clock types were already demonstrated to improve robustness of the generated time scale, ensembles using different clock types can clearly benefit from the advantages of the individual single clocks contributing to the time generation process. In particular, the performance of the ensemble time can be improved over a wide range of averaging times by combining clocks exhibiting superior stabilities for distinct time scales. In future, this approach could be used to integrate newly developed clock types such as e.g. optical clocks into a clock ensemble.
Multi‐level reranking approach for bug localization

Bug fixing has a key role in software quality evaluation. Bug fixing starts with the bug localization step, in which developers use textual bug information to find location of source codes which have the bug. Bug localization is a tedious and time consuming process. Information retrieval requires understanding the programme's goal, coding structure, programming logic and the relevant attributes of bug. Information retrieval (IR) based bug localization is a retrieval task, where bug reports and source files represent the queries and documents, respectively. In this paper, we propose BugCatcher, a newly developed bug localization method based on multi‐level re‐ranking IR technique. We evaluate BugCatcher on three open source projects with approximately 3400 bugs. Our experiments show that multi‐level reranking approach to bug localization is promising. Retrieval performance and accuracy of BugCatcher are better than current bug localization tools, and BugCatcher has the best Top N, Mean Average Precision (MAP) and Mean Reciprocal Rank (MRR) values for all datasets.
Towards a broadband and squint-free Ku-band phased array antenna system for airborne satellite communications

In this paper, we describe the design and the development of a Ku-band phased array antenna system for the reception of a digital video broadcasting by satellite (DVB-S) signal. A concept of optical beamforming is implemented to provide a squint-free beam steering over the entire Ku-band (10.7–12.75 GHz) as well as to achieve seamless tunability of the beam pointing direction. The total antenna system is described and the system performance is simulated. Requirements for system components are formulated and the development of these components towards the implementation of the broadband, squint-free phased array antenna system is reported.
IP-based IMT network platform

This article describes a network platform with future IP-based techniques for "beyond IMT-2000. " First, it presents a vision for beyond IMT-2000 in terms of requirements for service and network capabilities. Next, it shows a general architecture of the IP-based IMT network platform (IP/sup 2/). Then it discusses the study of key network techniques (location management, routing/handover, and service management) featured in the proposed platform architecture.
Using ecological restoration to constrain biological invasion

Summary 1 Biological invasion can permanently alter ecosystem structure and function. Invasive species are difficult to eradicate, so methods for constraining invasions would be ecologically valuable. We examined the potential of ecological restoration to constrain invasion of an old field by Agropyron cristatum, an introduced C3 grass. 2 A field experiment was conducted in the northern Great Plains of North America. One-hundred and forty restored plots were planted in 1994–96 with a mixture of C3 and C4 native grass seed, while 100 unrestored plots were not. Vegetation on the plots was measured periodically between 1994 and 2002. 3 Agropyron cristatum invaded the old field between 1994 and 2002, occurring in 5% of plots in 1994 and 66% of plots in 2002, and increasing in mean cover from 0·2% in 1994 to 17·1% in 2002. However, A. cristatum invaded one-third fewer restored than unrestored plots between 1997 and 2002, suggesting that restoration constrained invasion. Further, A. cristatum cover in restored plots decreased with increasing planted grass cover. Stepwise regression indicated that A. cristatum cover was more strongly correlated with planted grass cover than with distance from the A. cristatum source, species richness, percentage bare ground or percentage litter. 4 The strength of the negative relationship between A. cristatum and planted native grasses varied among functional groups: the correlation was stronger with species with phenology and physiology similar to A. cristatum (i.e. C3 grasses) than with dissimilar species (C4 grasses). 5 Richness and cover of naturally establishing native species decreased with increasing A. cristatum cover. In contrast, restoration had little effect on the establishment and colonization of naturally establishing native species. Thus, A. cristatum hindered colonization by native species while planted native grasses did not. 6 Synthesis and applications. To our knowledge, this study provides the first indication that restoration can act as a filter, constraining invasive species while allowing colonization by native species. These results suggest that resistance to invasion depends on the identity of species in the community and that restoration seed mixes might be tailored to constrain selected invaders. Restoring areas before invasive species become established can reduce the magnitude of biological invasion.
No association between ACE gene variation and endurance athlete status in Ethiopians.

PURPOSE The most widely studied candidate gene for endurance performance is the angiotensin-converting enzyme (ACE) gene. The best endurance runners in the world hail from Kenya and Ethiopia, so the lack of association between the ACE gene and elite endurance athlete status we previously reported in Kenyans requires replication in Ethiopians. METHODS DNA was extracted from buccal swabs collected from subjects filling four groups: elite endurance runners from the Ethiopian national athletics team specializing in 5 km to marathon distances (n = 76), controls demographically matched to the elite endurance athletes (n = 410), controls representing the general Ethiopian population (n = 317), and sprint and power event athletes from the Ethiopian national athletics team (n = 38). ACE I/D and A22982G (rs4363) genotype frequencies were determined for each of these groups, and differences between groups were assessed using χ(2) tests. RESULTS There were no significant deviations from Hardy-Weinberg equilibrium in endurance athletes or either control group. Endurance athletes did not differ significantly in ACE I/D genotype frequency when compared with the endurance athlete-matched control group (P = 0.16), general controls (P = 0.076), or sprint and power athletes (P = 0.39) (endurance athletes: 15.8% II, endurance athlete-matched controls: 8.8% II, general controls: 7.6% II, sprint and power athletes: 10.5% II). Similarly, no significant differences were found in ACE A22982G genotype between groups (endurance athletes: 13.2% AA, endurance athlete-matched controls: 12.2% AA, general controls: 12.0% AA, sprint and power athletes: 13.2%; endurance athletes vs endurance athlete-matched controls: P = 0.97, endurance athletes vs general controls: P = 0.95, endurance athletes vs sprint and power athletes: P = 0.52). CONCLUSIONS As previously shown in elite Kenyan athletes, ACE I/D and A22982G polymorphisms are not associated with elite endurance athlete status in Ethiopians.
Plasmid DNA Supercoiling and Survival in Long-Term Cultures of Escherichia coli: Role of NaCl

ABSTRACT The relationship between the survival of Escherichia coli during long-term starvation in rich medium and the supercoiling of a reporter plasmid (pBR322) has been studied. In aerated continuously shaken cultures, E. coli lost the ability to form colonies earlier in rich NaCl-free Luria-Bertani medium than in NaCl-containing medium, and the negative supercoiling of plasmid pBR322 declined more rapidly in the absence of NaCl. Addition of NaCl at the 24th hour restored both viability and negative supercoiling in proportion to the concentration of added NaCl. Addition of ofloxacin, a quinolone inhibitor of gyrase, abolished rescue by added NaCl in proportion to the ofloxacin added. This observation raises the possibility that cells had the ability to recover plasmid supercoiling even if nutrients were not available and could survive during long-term starvation in a manner linked, at least in part, to the topological state of DNA and gyrase activity.
Lipopolysaccharide, a Key Molecule Involved in the Synergism between Temporins in Inhibiting Bacterial Growth and in Endotoxin Neutralization*

Lipopolysaccharide (LPS) is the major structural component of the outer membrane of Gram-negative bacteria and shields them from a variety of host defense factors, including antimicrobial peptides (AMPs). LPS is also recognized by immune cells as a pathogen-associated molecular pattern and stimulates them to secrete pro-inflammatory cytokines that, in extreme cases, lead to a harmful host response known as septic shock. Previous studies have revealed that a few isoforms of the AMP temporin, produced within the same frog specimen, can synergize to overcome bacterial resistance imposed by the physical barrier of LPS. Here we found that temporins can synergize in neutralizing the LPS-induced macrophage activation. Furthermore, the synergism between temporins, to overcome the protective function of LPS as well as its endotoxic effect, depends on the length of the polysaccharide chain of LPS. Importantly, mode of action studies, using spectroscopic and thermodynamic methods, have pointed out different mechanisms underlying the synergism of temporins in antimicrobial and anti-endotoxin activities. To the best of our knowledge, such a dual synergism between isoforms of AMPs from the same species has not been observed before, and it might explain the ability of such amphibians to resist a large repertoire of microorganisms.
Intramam-Relationship between results of in vitro susceptibility tests and outcomes following treatment with pirlimycin hydrochloride in cows with subclinical mastitis associated with gram-positive pathogens

M is characterized by inflammation of the mammary gland and is almost always caused by a bacterial infection. Approximately 60% to 70% of new infections that develop during lactation do not cause obvious clinical signs and are often unrecognized. These subclinical infections are a serious concern for dairy farmers because of decreased milk production, reduced milk quality, and increased transmission of pathogens that cause mastitis. Antimicrobials are routinely used for treatment of dairy cattle affected with clinical and subclinical infections. Intramammary administration is used for approximately two-thirds of antimicrobials used for treatment of cows with mastitis. Intramammary treatments concentrate the drug at the site of infection and have limited systemic absorption of the drug, thus reducing the probability of unwanted adverse effects. IntramamRelationship between results of in vitro susceptibility tests and outcomes following treatment with pirlimycin hydrochloride in cows with subclinical mastitis associated with gram-positive pathogens