Miracle-dz/UniFAR-FTUs huggingface dataset:
Cultivation-Dependent and -Independent Approaches for Determining Bacterial Diversity in Heavy-Metal-Contaminated Soil

ABSTRACT In recent years, culture-independent methods have been used in preference to traditional isolation techniques for microbial community analysis. However, it is questionable whether uncultured organisms from a given sample are important for determining the impact of anthropogenic stress on indigenous communities. To investigate this, soil samples were taken from a site with patchy metal contamination, and the bacterial community structure was assessed with a variety of approaches. There were small differences in microscopic epifluorescence bacterial counts. Denaturing gradient gel electrophoresis (DGGE) profiles of 16S rRNA gene fragments (16S-DGGE) amplified directly from soil samples were highly similar. A clone library generated from the most contaminated sample revealed a diverse bacterial community, which showed similarities to pristine soil communities from other studies. However, the proportion of bacteria from the soil samples that were culturable on standard plate-counting media varied between 0.08 and 2.2%, and these values correlated negatively with metal concentrations. The culturable communities from each sample were compared by 16S-DGGE of plate washes and by fatty acid profiling of individual isolates. Each approach indicated that there were considerable differences between the compositions of the culturable communities from each sample. DGGE bands from both culture-based and culture-independent approaches were sequenced and compared. These data indicated that metal contamination did not have a significant effect on the total genetic diversity present but affected physiological status, so that the number of bacteria capable of responding to laboratory culture and their taxonomic distribution were altered. Thus, it appears that plate counts may be a more appropriate method for determining the effect of heavy metals on soil bacteria than culture-independent approaches.
Emergence and refinement of clustered horizontal connections in cat striate cortex

Pyramidal cells in layer 2/3 of adult cat striate cortex have long, intrinsic horizontal axon collaterals within both layer 2/3 and layer 5. These collaterals form periodic “clusters” of finer axon branches that link columns of similar orientation selectivity. We have investigated the sequence of events and possible mechanisms underlying the development of these clustered intrinsic horizontal connections using a combination of neuronal tracers and intracellular staining. Small injections of fluorescent latex microspheres made during the first postnatal week (at P4–6), when examined in tangential sections, produced an even, unclustered distribution of retrogradely labeled cells up to 2 mm from the injection site. At P8, retrograde labeling extended over a larger area and clustering was discernible, primarily among the most distant labeled cells. At both P6 and P8, labeling was similar in layers 2/3 and 5, indicating that the transition from clustered to unclustered connections occurred simultaneously for cells in superficial and deep laminae. By the end of the second postnatal week (P12–15), retrogradely labeled cells were far more clustered both within and beyond the extent of P6 label; the density of labeled cells was high throughout the labeled region, but much higher within clusters. The periodicity of these nascent clusters was similar to that in the adult. Despite obvious clustering, the pattern of retrograde label observed following injections at 2–3 weeks (P12–21) differed markedly from the adult, in that the regions between clusters contained many labeled cells. Over the next 3 weeks, the connections were refined, so that by the sixth postnatal week (P36–38), regions between clusters contained very few retrogradely labeled cells and the overall pattern of retrograde label was indistinguishable from that in adults. Despite differences in postmigratory ages of neurons from the superficial and deep laminae, clustering of retrogradely labeled cells from these 2 populations was similar at all ages. Experiments in which 2–3 weeks elapsed between the time microsphere injections were made and animals were killed demonstrated that neither the initial formation of crude clusters nor their refinement was due to cell death. Instead, cluster refinement resulted from specific process elimination. When a red microsphere injection at P15 was followed by a green microsphere injection at exactly the same location on P29, the earlier injection resulted in crude clustering, as expected. Virtually all of the cells double-labeled by the later injection were within the densest clusters of label from the early injection. (ABSTRACT TRUNCATED AT 400 WORDS)
Cannabis arteritis

Cannabis is the most consumed psychoactive substance by young people. Chronic use of cannabis can lead to cannabis arteritis, which is a very rare peripheral vascular disease similar to Buerger's disease. It is affecting young adults, especially men, consuming cannabis. A 27-year old woman, with no particular past medical history except for long-term use of cannabis and tobacco developed a digital necrosis in the left hand. She denied using other illicit drugs. Doppler ultrasound examination of the upper limbs was unremarkable. Toxicological analysis revealed the presence of cannabis in both biological fluid and hair strand. Despite medical treatment, cessation of the cannabis and tobacco consumption and hyperbaric oxygen therapy, an amputation of necrotic parts was then required. This case shows the prolonged use of cannabis could be a risk factor for young adult arteritis. Faced with a rapidly progressive arteritis occurring in young adult, the physician should consider the history of use of cannabis. Hair analysis can be useful for confirmation of the chronic consumption of drugs.
Effects of varying forage types on milk production responses to whole cottonseed, tallow, and yeast.

Four forage treatments (45% corn silage, 33.75% corn silage plus 11.25% alfalfa hay, 11.25% bermudagrass hay, or 11.25% cottonseed hulls on a DM basis) were arranged factorially with no added fat, 12.5% whole cottonseed, or 2.5% tallow. Different diets were fed during three 28-d periods to 20 control Holstein cows and to 20 cows receiving yeast continuously in a split-plot design. Milk yield of cows fed cottonseed hulls with corn silage was 2.4 kg/d higher than with corn silage plus bermudagrass hay and . 7 kg/d higher than with corn silage only or corn silage plus alfalfa hay. Whole cottonseed depressed milk yield by 1 kg/d. Cows fed yeast had increased DMI, and yeast interacted with forage so that more milk was produced by cows fed alfalfa diets. Yeast depressed milk protein percentage. Holstein cows in a commercial Florida dairy were fed no yeast or 10 g/d continuously for 60 d; milk fat percentage was greater (3.51 vs. 3.37%) with yeast. In summary, effects on milk and SCM were positive when cottonseed hulls were utilized with corn silage, negative with whole cottonseed, and neutral with supplemental tallow. Yeast effects on SCM, although not significant for either experiment, tended to be positive for both (mean +1.2 kg/d per cow).
Development of a novel enzyme-linked immunosorbent assay to detect anti-IgG against swine hepatitis E virus

Swine hepatitis E virus (HEV) is widespread throughout pigs in both developing and industrialized countries. This virus is an important zoonotic agent and a public concern worldwide. Infected pigs are asymptomatic, so diagnosing swine HEV relies on detection of the virus or antibodies against the virus. However, several obstacles need to be overcome for effective and practical serological diagnosis. In this study, we developed an enzyme-linked immunosorbent assay (ELISA) that used a purified recombinant capsid protein of swine HEV. The potential clinical use of this assay was evaluated by comparing it with a commercial kit (Genelabs Technologies, Diagnostics, Singapore). Results of the ELISA were highly correlated with those of the commercial kit with a sensitivity of 97% and specificity of 95%. ROC (receiving operator characteristic) analysis of the ELISA data produced a value of 0.987 (95% CI, 0.977~0.998, p < 0.01). The cut-off value for the ELISA was also determined using negative pig sera. In summary, the HEV-specific ELISA developed in the present study appears to be both practical and economical.
Quantification of HER2/neu gene amplification by competitive pcr using fluorescent melting curve analysis.

BACKGROUND Molecular detection methods for HER2/neu gene amplification include fluorescence in situ hybridization (FISH) and competitive PCR. We designed a quantitative PCR system utilizing fluorescent hybridization probes and a competitor that differed from the HER2/neu sequence by a single base change. METHODS Increasing twofold concentrations of competitor were coamplified with DNA from cell lines with various HER2/neu copy numbers at the HER2/neu locus. Competitor DNA was distinguished from the HER2/neu sequence by a fluorescent hybridization probe and melting curve analysis on a fluorescence-monitoring thermal cycler. The percentages of competitor to target peak areas on derivative fluorescence vs temperature curves were used to calculate copy number. RESULTS Real-time monitoring of the PCR reaction showed comparable relative areas throughout the log phase and during the PCR plateau, indicating that only end-point detection is necessary. The dynamic range was over two logs (2000-250 000 competitor copies) with CVs < 20%. Three cell lines (MRC-5, T-47D, and SK-BR-3) were determined to have gene doses of 1, 3, and 11, respectively. Gene amplification was detected in 3 of 13 tumor samples and was correlated with conventional real-time PCR and FISH analysis. CONCLUSION Use of relative peak areas allows gene copy numbers to be quantified against an internal competitive control in < 1 h.
Reductions between Expansion Problems

The Small-Set Expansion Hypothesis (Raghavendra, Steurer, STOC 2010) is a natural hardness assumption concerning the problem of approximating the edge expansion of small sets in graphs. This hardness assumption is closely connected to the Unique Games Conjecture (Khot, STOC 2002). In particular, the Small-Set Expansion Hypothesis implies the Unique Games Conjecture (Raghavendra, Steurer, STOC 2010). Our main result is that the Small-Set Expansion Hypothesis is in fact equivalent to a variant of the Unique Games Conjecture. More precisely, the hypothesis is equivalent to the Unique Games Conjecture restricted to instance with a fairly mild condition on the expansion of small sets. Alongside, we obtain the first strong hardness of approximation results for the Balanced Separator and Minimum Linear Arrangement problems. Before, no such hardness was known for these problems even assuming the Unique Games Conjecture. These results not only establish the Small-Set Expansion Hypothesis as a natural unifying hypothesis that implies the Unique Games Conjecture, all its consequences and, in addition, hardness results for other problems like Balanced Separator and Minimum Linear Arrangement, but our results also show that the Small-Set Expansion Hypothesis problem lies at the combinatorial heart of the Unique Games Conjecture. The key technical ingredient is a new way of exploiting the structure of the Unique Games instances obtained from the Small-Set Expansion Hypothesis via (Raghavendra, Steurer, 2010). This additional structure allows us to modify standard reductions in a way that essentially destroys their local-gadget nature. Using this modification, we can argue about the expansion in the graphs produced by the reduction without relying on expansion properties of the underlying Unique Games instance (which would be impossible for a local-gadget reduction).
Automated Romberg Testing in Patients With Benign Paroxysmal Positional Vertigo and Healthy Subjects

Objective: Benign paroxysmal positional vertigo (BPPV) is the most common cause of dizziness. The underlying pathomechanism responsible for the recurrent vertigo attacks has been elucidated in detail and highly effective treatment strategies (liberation maneuvers) have been developed. However, many BPPV patients complain about problems of balance especially following liberation maneuvers. Aim: To objectively demonstrate differences in balance performance in BPPV patients compared to healthy subjects both prior and after BPPV liberation maneuvers. Methods: Seven patients with BPPV of the posterior semicircular canal and nine healthy subjects participated. To assess balance while standing, we analyzed the location and temporal stability of the center of pressure recorded by pressure-sensitive electronic soles during Romberg testing (on stable ground and on foam) and tandem stand. To assess regularity of gait, we analyzed the step frequency during walking of 50 m. All tests were performed prior and after liberation maneuvers in both groups. Results: Healthy subjects and patients differ significantly in their balance performance and use different stabilization strategies both prior and after liberation maneuvers. Both Romberg tests indicated poorer balance in BPPV patients (mean COP shifted towards toes), especially in posttreatment tests, while tandem stand appeared unaltered. We did not observe differences in escorted (by an experimenter) walking regularities between patients and healthy subjects and between pre- and post-maneuver testing. Conclusion and significance: Our findings confirm the typical clinical observation of a further posttreatment deterioration of already impaired postural performance in BPPV patients. While the etiology and the time course of this peculiar problem warrants further studies, the treating physician should be familiar with this transient side effect of therapeutic maneuvers to provide adequate counseling of patients. Finally, we successfully demonstrated the pressure-sensitive electronic soles as a new and potentially useful tool for both clinical and research purposes.
Development of an antenna and multipath calibration system for Global Positioning System sites

Site‐dependent errors such as antenna phase‐center variations, multipath, and scattering can have a significant effect on high‐precision applications of the Global Positioning System (GPS). Determination of these errors has proven to be elusive since no method has been developed to measure these effects accurately in situ. We have designed and constructed a prototype Antenna and Multipath Calibration System (AMCS) to obtain such in situ corrections. The primary components of the AMCS are a steerable parabolic antenna, two GPS receivers, and a computer for control and data‐logging functions. We obtain phase corrections for site‐dependent errors by forming the difference between the carrier‐beat phases from the GPS antenna to be calibrated and from the AMCS antenna, which is relatively free of such errors. Preliminary “sky maps” of the antenna phase and multipath contributions show root‐mean‐square (RMS) phase variations that are a factor of 10 or more greater than the AMCS system noise, which is ∼0.5 mm. To explore the source of this “noise,” we acquired observations over small (few degrees) patches of the sky. From the analysis of these experiments we concluded that the source of the phase variations was antenna and multipath errors that vary by ∼5 mm amplitude over small changes in satellite direction. Thus, for example, differences of 1° in elevation angle can result in several millimeter variations in phase. Similarly, small variations in azimuth angle can also result in significant phase variations. We have also observed day‐to‐day millimeter‐level changes in the calibration. We hypothesize that these phase variations are due to changes in multipath caused by changes in the local electromagnetic environment associated with, e.g., weather.
Meningothelial Hamartoma Associated with Nevus Sebaceus

Meningothelial hamartoma is a rare lesion of ectopic meningothelial elements that usually presents on the scalp at birth or in early childhood. The characteristic spindle cells infiltrate through collagen and stain positively for epithelial membrane antigen and vimentin but are negative for CD31 and CD34. This distinguishes meningothelial hamartoma from vascular tumors. Nevus sebaceus is a fairly common lesion that has been associated with several different benign tumors, including trichoblastoma and syringocystadenoma papilliferum. We describe the case of a 17‐month‐old girl who presented with a meningothelial hamartoma in association with a nevus sebaceus. To the best of our knowledge, this is the second case reported.
Pathogenesis of coxsackievirus B2 in mice: characterization of clinical isolates of the coxsackievirus B2 from patients with myocarditis and aseptic meningitis in Korea

Group B coxsackieviruses (CVBs) are a group of common human pathogens producing various clinical symptoms. Although the virology of CVB is well known, there is limited information on viral pathogenesis and the relationship between clinical symptoms and viral phenotype, particularly for CVB type 2 (CVB2). In 2004 in Korea, two CVB2 strains were isolated: CB2/04/279 from stool of an acute myocarditis patient with heart failure and CB2/04/243 from an aseptic meningitis patient. In this study, a high degree of homology was observed between the CB2/04/279 and CB2/04/243 full genome sequences. The two Korean CVB2 isolates had 93.1% homology compared to 82.1%–82.5% nucleotide sequence identity with the cardiovirulence-associated reference CVB strain Ohio-1 (CVB/O). CVB2-induced pathogenesis was analyzed, focusing on virus-induced pathology of various tissues in 4-week-old BALB/c inbred male mice. Myocarditis developed and extensive pancreatic inflammation was observed in all mice infected with CB2/04/279 or CVB/O, but not in animals infected with CB2/04/243. This is the first report of the full-genomic sequence and pathogenesis of the CVB2 strain isolated from an acute myocarditis patient in Korea.
Significant role of an exocellular protease in utilization of heme by Vibrio vulnificus

Clinical and environmental isolates of Vibrio vulnificus could grow in a synthetic medium supplemented with heme protein as the iron source. Protease-deficient mutants of the bacterium could not utilize any of the heme proteins in the synthetic medium, but the addition of purified V. vulnificus protease restored their growth. The protease digested all heme proteins tested and elicited heme liberation from the proteins. Furthermore, the induction of protease production by the heme proteins was demonstrated. These observations suggest that protease contributes to the efficient utilization of heme by V. vulnificus.
Reverse data exchange: coping with nulls

An inverse of a schema mapping M is intended to "undo" what M does, thus providing a way to perform "reverse" data exchange. In recent years, three different formalizations of this concept have been introduced and studied, namely, the notions of an inverse of a schema mapping, a quasi-inverse of a schema mapping, and a maximum recovery of a schema mapping. The study of these notions has been carried out in the context in which source instances are restricted to consist entirely of constants, while target instances may contain both constants and labeled nulls. This restriction on source instances is crucial for obtaining some of the main technical results about these three notions, but, at the same time, limits their usefulness, since reverse data exchange naturally leads to source instances that may contain both constants and labeled nulls. We develop a new framework for reverse data exchange that supports source instances that may contain nulls, thus overcoming the semantic mismatch between source and target instances of the previous formalizations. The development of this new framework requires a careful reformulation of all the important notions, including the notions of the identity schema mapping, inverse, and maximum recovery. To this effect, we introduce the notions of extended identity schema mapping, extended inverse, and maximum extended recovery, by making systematic use of the homomorphism relation on instances. We give results concerning the existence of extended inverses and of maximum extended recoveries, and results concerning their applications to reverse data exchange and query answering. Moreover, we show that maximum extended recoveries can be used to capture in a quantitative way the amount of information loss embodied in a schema mapping specified by source-to-target tuple-generating dependencies.
Effect of delay on dynamic targets tracking performance and behavior in virtual environment

We analyze the impact of the delay between the sensors and the visualization on the performance at a catching task in virtual environment. Testers have been asked to interact with a virtual environment displayed on a 2D screen in front of them, catching, with the virtual hand, virtual balls falling from the top of the screen. Two thresholds have been inferred: a behavioral threshold delay beyond which the behavioral organization is sensibly affected and a performance threshold delay beyond which task performance begins to worsen. We found a drop in performance when the total delay is over 70–80 ms, yet without significant changes in the organization of successful catches. Although the presence of a threshold on behavior is still to be further investigated, these two thresholds give a practical indication for the design and the validation of virtual reality based training systems. This is especially important in the context of training human skills in virtual environment: in particular to assess the quality of a training platform simulating the three ball cascade juggling pattern.
LDLR–/–ApoB100/100 mice with insulin-like growth factor II overexpression reveal a novel form of retinopathy with photoreceptor atrophy and altered morphology of the retina

Purpose The aim of this study was to characterize the ocular morphology of low-density lipoprotein receptor–deficient apolipoprotein B-100-only mice, where overexpression of insulin-like growth factor II (IGF-II) has been shown to induce glucose intolerance and increase atherosclerotic lesion progression and calcification. Methods Fifteen-month-old mice were examined on a normal chow diet and after 3 months of a high-fat Western diet. IGF-II-negative LDLR–/–ApoB100/100 littermates and C57Bl/6J mice served as controls. In vivo color images of the fundi were obtained, and eyes were processed either for retinal flat mounts for assessment of neovascularization or for paraffin-embedded samples for immunohistochemical analyses. Results IGF-II overexpression and the resulting prediabetic phenotype did not induce microvascular damage when assessed in fundus photographs and retinal whole mounts, and the number of capillaries in IGF-II/LDLR–/–ApoB100/100 mice was not significantly different from LDLR–/–ApoB100/100 mice. However, morphology of the inner nuclear, outer plexiform, and outer nuclear layers was altered in the IGF-II/LDLR–/–ApoB100/100 mice. Moreover, photoreceptor atrophy and thinning of the outer nuclear layer were present. Caspase-3 staining was positive in the photoreceptor inner segment. In addition, retinas of the IGF-II/LDLR–/–ApoB100/100 mice displayed reduced rhodopsin positivity, consistent with the decreased number of photoreceptor cells. Conclusions This study reports a novel form of retinopathy with photoreceptor atrophy and abundant changes in retinal morphology in a mouse model of prediabetes and atherosclerosis.