Miracle-dz/UniFAR-FTUs huggingface dataset:
Moellerella wisconsensis, a new genus and species of Enterobacteriaceae found in human stool specimens

The name Moellerella wisconsensis is proposed for a group of the family Enterobacteriaceae previously called enteric group 46. The species name, wisconsensis, was coined because six of the nine strains were isolated in Wisconsin. M. wisconsensis strains were negative for indole production, Voges-Proskauer, H2S production, urea, phenylalanine deaminase, lysine and ornithine decarboxylases, arginine dihydrolase, gas production from D-glucose, acid production from trehalose, and motility; the strains were positive for methyl red, citrate (Simmons), and acid production from lactose and raffinose and resistant to colistin. DNAs from five strains of M. wisconsensis were highly related (80 to 93% in reactions assayed on hydroxyapatite at 60 degrees C and 78 to 97% at 75 degrees C) to 32P-labeled DNA of the proposed type strain (CDC 2896-78, ATCC 35017). Labeled DNA from this type strain was only 2 to 32% related (at 60 degrees C) to DNA from 49 strains of named and unnamed species of Enterobacteriaceae. Eight of nine M. wisconsensis strains were isolated from human stool samples. Clinical information on one strain was available, and it was found to be associated with a case of diarrhea. On MacConkey agar, colonies of M. wisconsensis were bright red with precipitated bile around them and thus were indistinguishable from Escherichia coli colonies. Future studies should focus on the isolation of this new organism and its relationship to human disease.
Terrestrial Small Mammals as Reservoirs of Mycobacterium ulcerans in Benin

ABSTRACT Mycobacterium ulcerans, the causative agent of Buruli ulcer (BU), is considered an environmental pathogen. Different mycobacteria were detected in 68 (12%) out of 565 small mammals collected in areas in Benin where BU is endemic. Although M. ulcerans was not found, we suggest that more research on M. ulcerans in African (small) mammals is needed.
Interaction in vitro of type III intermediate filament proteins with triplex DNA.

As previously shown, type III intermediate filaments (IFs) select from a mixture of linear mouse genomic DNA fragments mobile and repetitive, recombinogenic sequences that have also been identified in SDS-stable crosslinkage products of vimentin and DNA isolated from intact fibroblasts. Because these sequences also included homopurine.homopyrimidine (Pu.Py) tracts known to adopt triple-helical conformation under superhelical tension, and because IF proteins are single-stranded (ss) and supercoiled DNA-binding proteins, it was of interest whether they have a particular affinity for triplex DNA. To substantiate this, IF-selected DNA fragments harboring a (Pu.Py) segment and synthetic d(GA)(n) microsatellites were inserted into a vector plasmid and the constructs analyzed for their capacity to interact with IF proteins. Band shift assays revealed a substantially higher affinity of the IF proteins for the insert-containing plasmids than for the empty vector, with an activity decreasing in the order of vimentin > glial fibrillary acidic protein > desmin. In addition, footprint analyses performed with S1 nuclease, KMnO(4), and OsO(4)/bipyridine showed that the (Pu.Py) inserts had adopted triplex conformation under the superhelical strain of the plasmids, and that the IF proteins protected the triple-helical insert sequences from nucleolytic cleavage and chemical modification. All these activities were largely reduced in extent when analyzed on linearized plasmid DNAs. Because intramolecular triplexes (H-DNA) expose single-stranded loops, and the prokaryotic ssDNA-binding proteins g5p and g32p also protected at least the Pu-strand of the (Pu.Py) inserts from nucleolytic degradation, it seemed likely that the IF proteins take advantage of their ssDNA-binding activity in interacting with H-DNA. However, in contrast to g5p and E. coli SSB, they produced no clear band shifts with single-stranded d(GA)(20) and d(TC)(20), so that the interactions rather appear to occur via the duplex-triplex and triplex-loop junctions of H-DNA. On the other hand, the IF proteins, and also g32p, promoted the formation of intermolecular triplexes from the duplex d[A(GA)(20). (TC)(20)T] and d(GA)(20) and d(TC)(20) single strands, with preference of the Py (Pu.Py) triplex motif, substantiating an affinity of the proteins for the triplex structure as such. This triplex-stabilizing effect of IF proteins also applies to the H-DNA of (Pu.Py) insert-containing plasmids, as demonstrated by the preservation of intramolecular triplex-vimentin complexes upon linearization of their constituent supercoiled DNAs, in contrast to poor complex formation from free, linearized plasmid DNA and vimentin. Considering that (Pu.Py) sequences are found near MAR/replication origins, in upstream enhancer and promoter regions of genes, and in recombination hot spots, these results might point to roles of IF proteins in DNA replication, transcription, recombination, and repair.
Novel outer bounds for combination networks with end-user-caches

This paper studies the tradeoff between the memory size M and the download time / rate R∗ for networks where a server with N files is connected to H relays (without caches), which in turns are connected to K users equipped with caches of size M files. When each user is connected to a different subset of r relays, i.e., K = (Hr), the system is referred to as a combination network with end-user-caches. In this work, outer bounds are derived for the practically motivated case of uncoded cache contents, that is, bits of the various files are directly copied in the user caches without any coding. In this case, once the cache contents and the user demands are known, the problem reduces to a general index coding problem. This paper shows that relying on a well known “acyclic index coding outer bound” results in bounds that are not tight for combination networks with enduser-caches (as opposed to the case without relays) and provides two novel ways to derive the tightest known outer bounds to date. As a result of independent interest, an inequality that generalizes the well-known sub-modularity of entropy is derived.
Embracing the C preprocessor during refactoring

C preprocessor directives are heavily used in C programs because they provide useful and even necessary additions to the C language. However, they are usually executed and discarded before any analysis is applied on C programs. In refactoring, preprocessor directives must be preserved through the whole process of parsing, analysis and transformation to retain editable yet correct source code. We propose a new preprocessing approach and special program representations that allow a program to be analyzed and transformed without losing its preprocessor directives, but treating them as first‐class program entities. These representations are essential for a correct refactoring tool. We also describe the challenges that preprocessor directives bring to refactoring and how the program representations that we propose solve those challenges. Finally, we give details of two refactorings and present some case studies with our successfully applied solution. Copyright © 2013 John Wiley & Sons, Ltd.
Edaphic patterns as related to β-diversity in swamp forests and meadows of the lower Orinoco delta plain (Venezuela)

In the Neotropics, differences in phytogeographic patterns and species richness respond non-randomly to edaphic factors in many upland forests. However, whether wetland forests follow the same species differentiation patterns is not well known. In this paper we analyze the relationship among species occurrences and selected soil characteristics, particularly salinity and acidity, in several wetland plant communities. Plant specimens were collected and soil samples analyzed for exchangeable cations, chloride, and organic carbon. Statistical methods were applied to assess β-diversity and to detect relationships between patterns of floristic variation and spatial variations of the soil conditions. β-diversity was high among vegetation communities. Edaphic conditions were heterogeneous, and landward gradients were present only for salinity and some exchangeable bases. This resulted in a lack of a straightforward relationship of vegetation patterns to salinity. More than 30% of the reported species covaried with at least one of the three acidity-related variables, suggesting that some tolerance to deleterious effects of H+ and Al3+ at pH values < 4 is likely. Thus, in contrast to what we might expect in deltaic regions, acidity rather than salinity was the major factor driving species organization. However, variation of these soil characteristics taken together accounted for only 40% of floristic differences among communities.
The Kelch Protein KLHDC8B Guards against Mitotic Errors, Centrosomal Amplification, and Chromosomal Instability

Background: The large multinucleated Reed-Sternberg cell is the driving force behind Hodgkin lymphoma pathogenesis. Results: Disrupting KLHDC8B function leads to multinucleation, failed mitoses, centrosomal amplification, and aneuploidy, the major pathologic features of the Reed-Sternberg cell. Conclusion: KLHDC8B protects against mitotic errors and chromosomal instability. Significance: Midbody proteins play a previously unappreciated key role in Hodgkin lymphoma pathogenesis. The malignant cell in classical Hodgkin lymphoma (HL) is the binucleated giant Reed-Sternberg cell. Chromosomal instability and mitotic errors may contribute to HL pathogenesis; one potential mitotic regulator is the kelch protein KLHDC8B, which localizes to the midbody, is expressed during mitosis, and is mutated in a subset of familial and sporadic HL. We report that disrupting KLHDC8B function in HeLa cells, B lymphoblasts, and fibroblasts leads to significant increases in multinucleation, multipolar mitoses, failed abscission, asymmetric segregation of daughter nuclei, formation of anucleated daughter cells, centrosomal amplification, and aneuploidy. We recapitulated the major pathologic features of the Reed-Sternberg cell and concluded that KLHDC8B is essential for mitotic integrity and maintenance of chromosomal stability. The significant impact of KLHDC8B implicates the central roles of mitotic regulation and chromosomal segregation in the pathogenesis of HL and provides a novel molecular mechanism for chromosomal instability in HL.
SepMe: 2002 New visual separation measures

Our goal is to accurately model human class separation judgements in color-coded scatterplots. Towards this goal, we propose a set of 2002 visual separation measures, by systematically combining 17 neighborhood graphs and 14 class purity functions, with different parameterizations. Using a Machine Learning framework, we evaluate these measures based on how well they predict human separation judgements. We found that more than 58% of the 2002 new measures outperform the best state-of-the-art Distance Consistency (DSC) measure. Among the 2002, the best measure is the average proportion of same-class neighbors among the 0.35-Observable Neighbors of each point of the target class (short GONG 0.35 DIR CPT), with a prediction accuracy of 92.9%, which is 11.7% better than DSC. We also discuss alternative, well-performing measures and give guidelines when to use which.
Six-minute-walk test in chronic obstructive pulmonary disease: minimal clinically important difference for death or hospitalization.

RATIONALE Outcomes other than spirometry are required to assess nonbronchodilator therapies for chronic obstructive pulmonary disease. Estimates of the minimal clinically important difference for the 6-minute-walk distance (6MWD) have been derived from narrow cohorts using nonblinded intervention. OBJECTIVES To determine minimum clinically important difference for change in 6MWD over 1 year as a function of mortality and first hospitalization in an observational cohort of patients with COPD. METHODS Data from the ECLIPSE cohort were used (n = 2,112). Death or first hospitalization were index events; we measured change in 6MWD in the 12-month period before the event and related change in 6MWD to lung function and St. George's Respiratory Questionnaire (health status). MEASUREMENT AND MAIN RESULTS Of subjects with change in the 6MWD data, 94 died, and 323 were hospitalized. 6MWD fell by 29.7 m (SD, 82.9 m) more among those who died than among survivors (P < 0.001). A reduction in distance of more than 30 m conferred a hazard ratio of 1.93 (95% confidence interval, 1.29-2.90; P = 0.001) for death. No significant difference was observed for first hospitalization. Weak relationships only were observed with change in lung function or health status. CONCLUSIONS A reduction in the 6MWD of 30 m or more is associated with increased risk of death but not hospitalization due to exacerbation in patients with chronic obstructive pulmonary disease and represents a clinically significant minimally important difference.
Emotional Filters: Automatic Image Transformation for Inducing Affect

Current image transformation and recoloring algorithms try to introduce artistic effects in the photographed images, based on user input of target image(s) or selection of pre-designed filters. These manipulations, although intended to enhance the impact of an image on the viewer, do not include the option of image transformation by specifying the affect information. In this paper we present an automatic image-transformation method that transforms the source image such that it can induce an emotional affect on the viewer, as desired by the user. Our proposed novel image emotion transfer algorithm does not require a user-specified target image. The proposed algorithm uses features extracted from top layers of deep convolutional neural network and the user-specified emotion distribution to select multiple target images from an image database for color transformation, such that the resultant image has desired emotional impact. Our method can handle more diverse set of photographs than the previous methods. We conducted a detailed user study showing the effectiveness of our proposed method. A discussion and reasoning of failure cases has also been provided, indicating inherent limitation of color-transfer based methods in the use of emotion assignment.
The chicken ubiquitin gene contains a heat shock promoter and expresses an unstable mRNA in heat-shocked cells

A chicken genomic library was screened to obtain genomic clones for ubiquitin genes. Two genes that differ in their genomic location and organization were identified. One gene, designated Ub I, contains four copies of the protein-coding sequence arranged in tandem, while the second gene, Ub II, contains three. The origin of the two major mRNAs that are induced after heat shock in chicken embryo fibroblasts was determined by generating DNA probes from the 5'-and 3'-noncoding regions of the two genes. Both mRNAs are transcribed from Ub I, the larger being the unspliced precursor of the smaller. A 674-base-pair intron was located within the 5'-noncoding region of Ub I. The second gene, Ub II, does not appear to code for an RNA species in normal or heat-shocked chicken embryo fibroblasts. The expression of ubiquitin mRNA during heat shock and recovery was examined. Addition of actinomycin D before heat shock completely abolished the response of ubiquitin mRNA to the stress. Analysis of the stability of the mRNA during recovery revealed that the mRNA accumulated during the heat shock is rapidly degraded with a half-life of approximately 1.5 h, suggesting a specialized but transient role for ubiquitin during heat shock.
A simple modification for a longer and larger internal thoracic artery as a composite Y-graft

Abstract Objectives. Coronary artery bypass grafting (CABG) using bilateral internal thoracic artery (BITA) has been proven to improve survival. Many surgeons use the composite Y-graft which is made of left ITA (LITA) and right ITA (RITA) grafts. The LITA is typically anastomosed to left anterior descending artery (LAD). However, we have used RITA for LAD instead of LITA and reviewed the patency of ITA grafts and their clinical outcomes. Methods. We analyzed 48 patients who underwent CABG using a BITA composite Y-graft from 2002 to 2012. In 30, LITA was anastomosed to LAD (Group L). The other 18 had RITA to LAD anastomosis (Group R). Results. The mean age of Group R was higher than that of Group L (p = 0.009). Postoperative angiography was performed in 35 patients (73%). Two patients in Group L and none of the patients in Group R had an ITA graft failure. The incidence of ITA graft failure and new adverse cardiovascular events were not different between the two groups. Conclusion. The clinical outcome of RITA to LAD anastomosis is comparable with anastomosis of LITA to LAD in CABG using BITA composite Y-grafts. This technique may be useful when longer and larger ITA grafts are needed.
Design and testing of beta-actin primers for RT-PCR that do not co-amplify processed pseudogenes.

Quantitative reverse transcription polymerase chain reaction (RT-PCR) is being used increasingly as an alternative to Northern blots analysis or RNase protection assays for quantitation of gene expression. To quantify different samples, measurements are often normalized using the expression of so-called "housekeeping" genes, such as cytoplasmic beta-actin or glyceraldehyde-3-phosphate dehydrogenase. This approach can produce false results because the presence of processed pseudogenes in the genome, which are related to some of the commonly used transcripts of housekeeping genes, leads to co-amplification of contaminating genomic DNA. By yielding amplification products of the same or similar size as the reverse-transcribed target, mRNA quantitation of expression is prone to error. In this paper, we report the results of using three sets of beta-actin primers for RT-PCR in the presence and absence of genomic DNA. In addition, we propose two new pairs of oligonucleotide primers that specifically amplify the human and rat beta-actin reverse-transcribed mRNA but not pseudogene sequences. These primers are especially suitable for quantitation of mRNA in small tissue samples (e.g., biopsies), where DNase digestion is not feasible, and therefore DNA contamination cannot be avoided.
Introduction Osteoporosis in Surgical Menopause

Background: Osteoporosis in both surgical and natural menopausal women are common health hazards all over the world. And the surgical menopausal women may have the greater chance of this disorder than those of natural menopausal women. Objective: To observe osteoporotic changes in both surgical and natural menopausal women in Bangladesh. Method: This Cross sectional study was carried out in the Department of Physiology, Sir Salimullah Medical College, Dhaka between 1st January 2010 to 31st December 2010. A total number of 60 female subjects were included in this study. Among them 30 surgical menopausal women age ranged from 45-55 years were included in the study group (Group B) and 30 natural menopausal women age ranged from 50-60 years were taken as control (Group A). All the menopausal women were selected from Out Patient Department (OPD) of Gynaecology and Obstetrics, Sir Salimullah Medical College and Mitford Hospital. Estimation of serum estrogen level by microparticle enzyme immunoassay (MEIA) method and Tscore was obtained by Dual energy X-ray absorptiometry of both natural and surgical menopausal women were done. The statistical analysis was done by using appropriate method as applicable. Results: In this study Tscore of both spinal and femoral neck bone were significantly (p<0.001) lower in surgical menopausal women than those of natural menopausal women. Again, mean serum estrogen level was significantly (p<0.001) lower in surgical menopausal women than that of natural menopausal women. Conclusion: The present study revealed that surgical menopausal women have greater chance of osteoporosis than those of natural menopausal women.
Teleoperation system for multiple robots with HAM: free gait for following motion of quadruped robots

A purpose of our research is to realize a human adaptive teleoperation system for cooperative conveyance tasks by multiple robots. For such multiple robots operation task, an operator generally can operate only a few points and the robots have to follow the points with suitable formations. Therefore, the robot control scheme is required not only maneuverable but also to have a following ability. However, some constraints bring about difficulties for the motion. Especially, four constraints, which are stability, workspace constraint, obstacle avoidance, and a following to reference points with an interval, are critical. A lot of researchers have proposed the flexible gait patterns, called free gait, to improve the internal quadruped robot problems as stability and workspace constraints. However, few researchers have focused on following motion. Consequently, we propose a free gait pattern, which improves the conventional internal robot problems, and additionally has a following function by an artificial potential field approach. This paper addresses a gait pattern design with the following feature and experiments to verify it.
[Clinical possibility of low ligation of inferior mesenteric artery and lymph nodes dissection in laparoscopic low anterior resection].

OBJECTIVE To investigate the clinical possibility of low ligation of inferior mesenteric artery (IMA) and lymph nodes dissection in laparoscopic low anterior resection. METHODS Data was collected retrospectively from 216 patients who underwent laparoscopic low anterior resection in our hospital from June 2011 to January 2015.Patients were divided into control group (132 cases) and observation group (84 cases). The observation group was treated with low ligation of IMA and lymph nodes dissection, and the control group was cured by high ligation of IMA and lymph nodes dissection. We analyzed the operation time, the number of lymph nodes dissection, the number of lymph nodes removed around the root of IMA, the rate of lymph node metastasis around the root of IMA, the incidence of anastomotic leakage and the ventilation time after the operation. RESULTS There was no significant difference between the two group in the pre-operative data, operation time, the number of lymph nodes dissection the number of lymph nodes removed around the root of IMA, the rate of lymph node metastasis around the root of IMA and the incidence of anastomotic leakage (P>0.05). The observation group were significantly better than the control group the in the ventilation time after the operation (P<0.05). The follow up time was 12 to 67 months. The median follow up time was 37 months. One patient in observation group died of cardiovascular disease. One patient in control group died of metastatic carcinoma. CONCLUSION Detection of low ligation of inferior mesenteric artery and lymph nodes dissection in laparoscopic low anterior resection is safe and practicable, which should be widely applied.
Olfactory Learning-Set Formation in Rats

Rats trained on 16 two-odor discrimination problems showed rapid acquisition of a learning set and one-trial learning by the end of the problem series. Learning to sample odor cues before responding and adoption of a "win-stay, lose-shift" strategy probably accounts for the virtually errorless learning. Learning-set performance of rats trained with odor stimulus comparable to that reported for primates trained on visual cues.