Miracle-dz/UniFAR-FTUs huggingface dataset:
Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants[W][OA]

This study identifies regions of noncoding DNA in dicot plants that are likely to facilitate complex regulation of genes by binding multiple transcription factors. Regulatory mechanisms that the model organism Arabidopsis is likely to share with crop plants provide a focus for research that has real-world applications. Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.
Short Selling and Politically Motivated Negative Information Hoarding

Extant literature documents that managers have an incentive to hoard bad news due to political concerns. In this paper, we test the proposition that short selling has an attenuating effect on the politically motivated suppression of bad news. We examine the stock price behavior of Chinese public firms around two highly visible political events - meetings of the National Congress of the Chinese Communist Party and Two Sessions (The National People’s Congress Conference and The Chinese People’s Political Consultative Conference) from 2002-2014, and find that political bad news hoarding has been reduced after short selling becomes available. We establish causality by relying on a difference-in-differences approach based on a controlled experiment of short selling regulation changes in China. We also find this reduction in bad news hoarding to be more pronounced in firms with stronger political connection (higher state ownership and larger size) and higher accounting opacity, which further confirms our finding. This study sheds new light on the real effects of short sellers on political impact on capital market.
Etheliaceae fam. nov. (Gigartinales, Rhodophyta), with a clarification of the generitype of Ethelia and the addition of six novel species from warm waters

Based upon COI‐5P, LSU rDNA, and rbcL sequence data and morphological characteristics, six new members of the noncalcified crustose genus of red algae Ethelia are described in a new family, Etheliaceae (Gigartinales), sister to the recently described Ptilocladiopsidaceae. The novel species are described from subtropical to tropical Atlantic and Indo‐Pacific Ocean basins; E. mucronata sp. nov. and E. denizotii sp. nov. from southern and northern Western Australia respectively, E. wilcei sp. nov. from the Cocos (Keeling) Islands of Australia, E. suluensis sp. nov. from the Philippines, E. umbricola sp. nov. from Bermuda and E. kraftii sp. nov. from Lord Howe Island, Australia. The generitype, Ethelia biradiata, originally reported from the Seychelles, Indian Ocean, is added to the Western Australian flora.
Characterization of thermal field in mixed-convection cooling of a flat plate by an impinging slot jet

This paper deals with the experimental and numerical study of cooling effect in low-speed two-dimensional slot jet impinging on an isothermal vertical hot plate. The jet is discharged into a semi confined zone which is bounded with two parallel isothermal walls. Both top and bottom boundaries are open to the ambient air. The wall adjacent to the nozzle is kept at the same temperature of ambient whereas the target surface is heated to maintain a constant temperature difference with respect to the opposite wall. The range of the jet Reynolds number on the basis of nozzle hydraulic diameter is kept within the range of 92 to 553. This leads to velocities of the same order of magnitude to that of natural convection close to the target wall. As an accurate optical method, Interferometry has been selected for experimental study of the thermal field behavior and for measuring the local heat transfer coefficient. A specific method of interferogram analysis for flat surfaces has been utilized for data reduction. Also the numerical simulation of the problem has been done for solving the flow field and for comparing the theoretical heat transfer model with the obtained experimental data. A commercial CFD package (FLUENT 6) has been utilized as a solver that uses finite volume method (FVM) to solve the governing equation of the problem. Variations of jet Reynolds numbers (Re), Nozzle to plate spacing (Z) and the nozzle vertical distance from the plate leading edge (Y) have been considered.
Trajectories of illness perceptions in persons with chronic illness: An explorative longitudinal study

Accurate illness perceptions are essential to the self-management of chronic illness. This study explored trajectories of illness perceptions in persons with morbid obesity (n = 53) and persons with chronic obstructive pulmonary disease (n = 52) following a patient education course. Participants completed the Brief Illness Perception Questionnaire five times over a 1-year period. Repeated measures analysis of variance was employed. Over time, obese participants perceived shorter illness duration, fewer consequences, less emotional stress, and more personal control. Chronic obstructive pulmonary disease participants had initial increases in personal control and understanding, but these changes were not maintained throughout the follow-up period.
Readability of Narrative Disclosures in 10-K Reports: Does Managerial Ability Matter?

Abstract This study examines the association between managerial ability and the readability of narrative disclosures in 10-K reports. Using a large US sample from 1994 to 2015, we find that managerial ability is significantly positively associated with the readability of narrative disclosures in 10-K reports. We also find that this association is more pronounced for firms with high levels of profitability. In addition, firms’ financial performance mediates the association between managerial ability and the readability of 10-K reports. Further analysis shows that the association was more pronounced before the implementation of the plain English disclosure rules. These results are robust to alternative specifications of managerial ability, 10-K report readability, and the endogeneity concern. Overall, findings from this study suggest that managerial ability matters for improving the readability of corporate disclosures.
Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma.

BACKGROUND Accumulating evidence indicates that diet is one of the most important environmental factors involved in the progression from advanced colorectal adenoma (A-CRA) to colorectal cancer. OBJECTIVE We evaluated the possible effects of dietary fiber on the fecal microbiota of patients with A-CRA. DESIGN Patients with a diagnosis of A-CRA by pathological examination were enrolled in the A-CRA group. Patients with no obvious abnormalities or histopathological changes were enrolled in the healthy control (HC) group. Dietary fiber intake was assessed in all patients. Short-chain fatty acids (SCFAs) in feces were detected by gas chromatography. The fecal microbiota community was analyzed by 454 pyrosequencing based on 16S ribosomal RNA. RESULTS Lower dietary fiber patterns and consistently lower SCFA production were observed in the A-CRA group (n = 344). Principal component analysis showed distinct differences in the fecal microbiota communities of the 2 groups. Clostridium, Roseburia, and Eubacterium spp. were significantly less prevalent in the A-CRA group (n = 47) than in the HC group (n = 47), whereas Enterococcus and Streptococcus spp. were more prevalent in the A-CRA group (n = 47) (all P < 0.05). Butyrate and butyrate-producing bacteria were more prevalent in a subgroup of HC subjects with a high fiber intake than in those in both the low-fiber HC subgroup and the high-fiber A-CRA subgroup (all P < 0.05). CONCLUSION A high-fiber dietary pattern and subsequent consistent production of SCFAs and healthy gut microbiota are associated with a reduced risk of A-CRA. This trial was registered at www.chictr. org as ChiCTR-TRC-00000123.
Control Chart Tests Based on Geometric Moving Averages

A geometrical moving average gives the most recent observation the greatest weight. and all previous observations weights decreasing in geometric progression from the most recent back to the first. A graphical procedure for generating geometric moving averages is described in which the most recent observation is assigned a weight r. The properties of control chart tests based on geometric moving averages are compared to tests based on ordinary moving averages.
Evaluation of the ability of bone marrow derived cells to engraft the kidney and promote renal tubular regeneration in mice following exposure to cisplatin

Abstract It has been suggested that bone marrow derived stem cells have the ability to engraft the kidney and improve the outcome of severe acute kidney injury (AKI) in mice exposed to high doses of cisplatin, providing hope for cancer patients in whom irreversible renal damage occasionally occurs following the use of this highly effective anti-tumor drug. We tested the therapeutic potential of bone marrow derived cells injected during the acute phase (day 3 after cisplatin administration) of experimentally-induced AKI in C57Bl6/J mice, characterized by massive tubular necrosis, apoptosis, and a low proliferation capacity. We failed to show any benefit of bone marrow derived cells versus a regular homogenate of intact renal cells, or normal saline. Using cell tracers and flow cytometry, we demonstrated that bone marrow derived cells did indeed home to the bone marrow of the recipients but failed to settle in the kidney. Conversely, renal cells homed to injured kidneys. However, neither cell therapy protected the animals against cisplatin-induced death. We therefore question the short-term efficacy of bone marrow derived cells used to repair established injuries of the tubular epithelium.
Evaluation of Tobacco Control Policies in San Francisco Homeless Housing Programs

Background. The 2014 Surgeon General’s Report noted that high smoking rates in vulnerable populations such as the homeless have been a persistent public health problem; smoking prevalence among individuals experiencing homelessness exceeds 70%. Historically, service providers for the homeless have not enacted comprehensive tobacco control policies. Method. We conducted a qualitative study of homeless housing programs in San Francisco. Administrators representing 9 of the city’s 11 homeless service agencies were interviewed to assess institutional smoking-related policies and cessation programs and perceived barriers and receptivity to instituting tobacco control interventions. Results. Respondents indicated that although most programs had adopted smoke-free grounds and some had eliminated evidence of staff smoking, the smoking status of clients was assessed only when required by funders. None of the programs offered smoking cessation interventions. Most administrators were receptive to adopting policies that would promote a tobacco-free culture; however, they noted that their clients had unique challenges that made traditional smoking cessation programs unfeasible. Conclusions. Homeless housing programs in San Francisco have not yet adopted a tobacco-free culture. Existing policies were created in response to external mandates, and smoking cessation programs may need to be modified in order to effectively reach clients.
A Cognitive Model of Generalized Anxiety Disorder

One possible alternative to standard in vivo exposure may be virtual reality exposure. Virtual reality integrates real-time computer graphics, body tracking devices, visual displays, and other sensory input devices to immerse a participant in a computer-generated virtual environment. Virtual reality exposure (VRE) is potentially an efficient and cost-effective treatment of anxiety disorders.VRE therapy has been successful in reducing the fear of heights in the first knowncontrolled study of virtual reality in the treatment of a psychological disorder. Outcome was assessed on measures of anxiety, avoidance, attitudes, and distress. Significant group differences were found on all measures such that theVREgroupwas significantly improved at posttreatment but the control group was unchanged. The efficacy of virtual reality exposure therapy was also supported for the fear of flying in a case study. The potential for virtual reality exposure treatment for these and other disorders is explored.
Clinical application of faecal calprotectin in ulcerative colitis patients

Objective Faecal calprotectin (FC) is the most relevant noninvasive biomarker for monitoring inflammatory status, response to treatment and for predicting clinical relapse in ulcerative colitis (UC). The aim of this study was to evaluate the role of FC in predicting both clinical/endoscopic activity and clinical relapse in a large UC patient cohort. Patients and methods A two-phase prospective study was carried out. In the first phase, the relationship between FC and clinical/endoscopic activity was evaluated. In the second phase, a cohort of asymptomatic patients with endoscopic mucosal healing was followed up using clinical and FC level determinations. Results One hundred and twenty-one UC patients were enrolled. The FC concentrations were directly correlated with both clinical and endoscopic activity (r=0.76 and 0.87, respectively, P<0.05) and were capable of differentiating between different degrees of endoscopic severity (P<0.01). An FC cut-off value of 110 &mgr;g/g was highly predictive (95%) of endoscopic activity. Seventy-four patients in clinical remission with mucosal healing were followed up for a year or until relapse and 27% developed a clinical relapse. The FC concentration of nonrelapsed patients (48 &mgr;g/g) versus relapsed patients (218 &mgr;g/g) was significantly different (P<0.01). An FC cut-off value of 193 &mgr;g/g had an accuracy of 89% in predicting clinical relapse. High FC levels were associated with clinical relapse using survival analysis and multivariate analysis. Conclusion Our data strongly support the use of FC for staging the activity of disease, predicting relapse and leading decision-making in a UC setting.
Functional level of young adults with cerebral palsy

Objective: To acquire insight into the level of functioning of young adults with cerebral palsy (CP). Design: Descriptive cross-sectional study. Setting: Rehabilitation Centre Den Haag, The Netherlands. Method: A structured questionnaire, including the Barthel Index was mailed to 134 young adults (aged 21–31 years) with cerebral palsy. Results: Eighty subjects responded (60%). Of these, 60 (75%) were largely or fully independent in activities of daily living, 72 (90%) moved independently indoors, 56 (70%) outdoors. In 67 (77.5%) of the group the level of communication was adequate for telephone conversation. Twenty-four (30%) lived with their parents, 10 (12.5%) with a partner and 26 (32.5%) lived alone. Almost half lived in an unadapted house. Forty-two (53%) completed some form of secondary education and 29 (36.3%) had paid employment. Conclusion: Despite their considerable impairments, the large majority of this group of young adults with cerebral palsy are independent in activities of daily living, mobility and communication. Regarding the level of education, participation in paid employment and sports activities, however, young adults with CP are poorly integrated.
Aspect mining using model-based clustering

Legacy systems contain critical and complex business code that has been in use for a long time. This code is difficult to understand, maintain, and evolve, in large part due to crosscutting concerns: software system features, such as persistence, logging, and error handling, whose implementation is spread across multiple modules. Aspect-oriented techniques separate crosscutting concerns from the base code, using separate modules called aspects and, thus, simplify the legacy code. Aspect mining techniques identify aspect candidates so that the legacy code can then be refactored into aspects. This study shows that model-based clustering using a carefully selected vector-space of features can be more effective than extant aspect mining methods based on heuristic methods as such hierarchical or partitional clustering. Three model-based algorithms were experimentally compared against existing heuristic methods, such as k-means clustering and agglomerative hierarchical clustering, using six different vector-space models. Model-based algorithms performed better in not spreading the methods of the concerns across the multiple clusters and were significantly better at partitioning the data such that, given an ordered list of clusters, fewer clusters and methods were needed to be analyzed to find all the concerns. In addition, model-based algorithms automatically determined the optimal number of clusters, a great advantage over the heuristic-based algorithms. Lastly, the newly defined vector-space models performed better, relative to aspect mining, than the previously defined vector-space models.
Quantitative T2 Mapping of Matrix-Associated Autologous Chondrocyte Transplantation at 3 Tesla: An In Vivo Cross-Sectional Study

Objectives:To evaluate magnetic resonance (MR) T2 mapping for characterization of cartilage repair tissue following matrix-associated autologous cartilage transplantation (MACT). Materials and Methods:Fifteen patients were evaluated following MACT using a 3T MR scanner. Patients were categorized into 2 postoperative intervals: I: 3–13 months, II: 19–42 months. Mean T2 relaxation times calculated from multiple spin-echo sequence were determined in regions of interest (MACT and normal hyaline cartilage) and T2 line profiles through the repair tissue and control sites were acquired. Results:Mean global T2 values of repair tissue in group I were significantly higher than at control sites (P < 0.05). Repair tissue in group II showed no significant difference to control sites. Repair tissue T2 line profiles normalized over time toward the control sites. Conclusions:T2 mapping allows visualization of cartilage repair tissue maturation. Global T2 repair tissue values approach that of control sites after more than 1.5 years, similar behavior is seen in the zonal organization.
A 2×2 80 Gbps 215-1 PRBS generator with three operational modes and a clock divider

An 80 Gbps 215-1 pseudo-random bit sequence (PRBS) generator offering a unique feature of two programmable channels is presented. It is possible to select either a replica of the full rate stream, two parallel streams at half the rate, or a combination of external and internal pattern to the output. This flexibility makes the design suitable for generating proper test signal for both binary and 4-PAM (pulse-amplitude-modulation) communication systems. While the longer sequence in this design adds to the complexity, the energy per bit is comparable with the state-of-the-art designs. Notably for the clock drivers, as one of the bottlenecks of a PRBS generator, an open-collector structure with distributed loading is studied and optimized for very low power operation. The design features a clock divider and zero detection circuit as well. The circuit was fabricated in a 130 nm SiGe BiCMOS process (300/500 GHz fr/fmax).
Effects of Mycobacterium bovis BCG Infection on Regulation of l-Arginine Uptake and Synthesis of Reactive Nitrogen Intermediates in J774.1 Murine Macrophages

ABSTRACT The generation of nitric oxide (NO) by activated macrophages is believed to control mycobacterial infection in the murine system. In this study we examined the effect ofMycobacterium bovis BCG infection on thel-arginine-dependent NO pathway in J774.1 murine macrophages. We have confirmed previous results by demonstrating that stimulation of J774.1 with lipopolysaccharide (LPS) and gamma interferon (IFN-γ) results in an increase in the uptake of3H-labeled l-arginine and a concomitant increase in the production of NO. We have also shown that BCG can mimic LPS treatment, leading to enhancedl-[3H]arginine uptake by IFN-γ-stimulated macrophages. Lipoarabinomannan, a component of the BCG cell wall that is structurally similar to LPS, is not responsible for the uptake stimulation in IFN-γ stimulated macrophages. Although we demonstrated that there was a 2.5-fold increase in NO production by macrophages 4 h after LPS–IFN-γ stimulation, BCG infection (with or without IFN-γ stimulation) did not lead to the production of NO by the macrophages by 4 h postinfection. At 24 h postinfection, the infected macrophages that were stimulated with IFN-γ produced amounts of NO similar to those of macrophages stimulated with LPS–IFN-γ. This suggests that there are multiple regulatory pathways involved in the production of NO. Finally, our data suggest that increased expression of the arginine permease, MCAT2B, after 4 h of LPS–IFN-γ treatment or BCG infection–IFN-γ treatment is not sufficient to account for the increases in l-[3H]arginine uptake detected. This suggests that the activity of the l-arginine transporter(s) is also altered in response to macrophage activation.
Not All Floating‐Harbor Syndrome Cases are Due to Mutations in Exon 34 of SRCAP

Floating‐Harbor syndrome (FHS) is a rare disorder characterized by short stature, delayed bone age, speech delay, and dysmorphic facial features. We report here the molecular analysis of nine cases, fulfilling the diagnostic criteria for FHS. Using exome sequencing, we identified SRCAP as the disease gene in two cases and subsequently found SRCAP truncating mutations in 6/9 cases. All mutations occurred de novo and were located in exon 34, in accordance with the recent report of Hood et al. However, the absence of SRCAP mutations in 3/9 cases supported genetic heterogeneity of FH syndrome. Importantly, no major clinical differences were observed supporting clinical homogeneity in this series of FHS patients.
Colorimetric Detection of Polynucleotides on Polypropylene Slices

The gold-label-silver-stain method (GLSS) for DNA hybridization detection has been receiving increased interest as a colorimetric detective method, demonstrating the advantages of non-radioactivity, non-quenching effect of fluorescence and simplicity for analytical equipment. A colorimetric detection based on the GLSS method was applied to DNA arrays in situ synthesized on polypropylene (PP) slices. In this paper a simple plasma treatment was employed to graft amino (-NH_2) on the polypropylene slice surfaces, where DNA probes were immobilized via in situ synthesis. Hybridization was accomplished by a sandwich hybridization format. With the amplification of Silver Enhancer Solution, the hybridization signals were recorded with a scanner. A target DNA concentration as low as 100 fM was detected. Complementary and mismatched sequences were clearly distinguished, and the ratio of the background-subtracted gray scale values for a perfect match, single-base mismatch, 2-base mismatch and 3-base mismatch is 22:16:9:4. The sensitivity of the in situ synthesis system was 3 orders of magnitude higher than that of the spotting system, and the signals of the former were about 2-times stronger than that of the latter under the same target DNA concentration.