Miracle-dz/UniFAR-FTUs huggingface dataset:
Perception of biological motion without local image motion

A vivid perception of the moving form of a human figure can be obtained from a few moving light points on the joints of the body. This is known as biological motion perception. It is commonly believed that the perception of biological motion rests on image motion signals. Curiously, however, some patients with lesions to motion processing areas of the dorsal stream are severely impaired in image motion perception but can easily perceive biological motion. Here we describe a biological motion stimulus based on a limited lifetime technique that tests the perception of a moving human figure in the absence of local image motion. We find that subjects can spontaneously recognize a moving human figure in displays without local image motion. Their performance is very similar to that for classic point-light displays. We also find that tasks involving the discrimination of walking direction or the coherence of a walking figure can be performed in the absence of image motion. Thus, although image motion may generally aid processes such as segmenting figure from background, we propose that it is not the basis for the percept of biological motion. Rather, we suggest biological motion is derived from dynamic form information on body posture evolving over time.
Frequency of orthodontic extraction

Introduction: The option of dental extraction for orthodontic purposes has been debated for more than 100 years, including periods when it was widely used in treatment, including the present, during which other methods are used to avoid dental extractions. The objective was to analyze the frequency of tooth extraction treatment performed between 1980 and 2011 at the Orthodontic Clinic of Universidade Estadual do Rio de Janeiro (UERJ). Material and Methods: The clinical records of 1484 patients undergoing orthodontic treatment were evaluated. The frequency of extractions was evaluated with regard to sex, Angle's classification, the different combinations of extractions and the period when orthodontic treatment began. Chi-square test was used to determine correlations between variables, while the chi-square test for trends was used to assess the frequency of extractions over the years. Results: There was a reduction of approximately 20% in the frequency of cases treated with tooth extraction over the last 32 years. The most frequently extracted teeth were first premolars. Patients with Class I malocclusion showed fewer extractions, while Class II patients underwent a higher number of extraction treatment. There were no statistically significant differences with regard to sex. Conclusion: New features introduced into the orthodontic clinic and new esthetic concepts contributed to reducing the number of cases treated with dental extractions. However, dental extractions for orthodontic purposes are still well indicated in certain cases.
Substantial within-Animal Diversity of Salmonella Isolates from Lymph Nodes, Feces, and Hides of Cattle at Slaughter

ABSTRACT Lymph nodes (mandibular, mesenteric, mediastinal, and subiliac; n = 68) and fecal (n = 68) and hide (n = 35) samples were collected from beef carcasses harvested in an abattoir in Mexico. Samples were analyzed for Salmonella, and presumptive colonies were subjected to latex agglutination. Of the isolates recovered, a subset of 91 was characterized by serotyping, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility phenotyping. Salmonella was isolated from 100% (hide), 94.1% (feces), 91.2% (mesenteric), 76.5% (subiliac), 55.9% (mandibular), and 7.4% (mediastinal) of samples. From the 87 typeable isolates, eight Salmonella enterica serotypes, including Kentucky (32.2%), Anatum (29.9%), Reading (17.2%), Meleagridis (12.6%), Cerro (4.6%), Muenster (1.1%), Give (1.1%), and Mbandaka (1.1%), were identified. S. Meleagridis was more likely (P = 0.03) to be recovered from lymph nodes than from feces or hides, whereas S. Kentucky was more likely (P = 0.02) to be recovered from feces and hides than from lymph nodes. The majority (59.3%) of the Salmonella isolates were pansusceptible; however, multidrug resistance was observed in 13.2% of isolates. Typing by PFGE revealed that Salmonella strains generally clustered by serotype, but some serotypes (Anatum, Kentucky, Meleagridis, and Reading) were comprised of multiple PFGE subtypes. Indistinguishable PFGE subtypes and, therefore, serotypes were isolated from multiple sample types, and multiple PFGE subtypes were commonly observed within an animal. Given the overrepresentation of some serotypes within lymph nodes, we hypothesize that certain Salmonella strains may be better at entering the bovine host than other Salmonella strains or that some may be better adapted for survival within lymph nodes. Our data provide insight into the ecology of Salmonella within cohorts of cattle and offer direction for intervention opportunities.
Hepatitis B Virus Drug Resistance Tools: One Sequence, Two Predictions

Drug resistance testing, genotype analysis, and the determination of immune and vaccine escape variants support personalized antiviral treatment for hepatitis B patients. As phenotypic drug resistance testing for hepatitis B virus (HBV) is especially labor-intensive, due to the lack of simple cell culture systems, genotypic methods play a very pronounced role. The genetic structure of HBV allows the simultaneous analysis of two different genes by examination of a single region in the genome of HBV. Nevertheless, the overlapping open reading frames of the hepatitis B surface antigen (HBsAg) and the reverse transcriptase (RT) have to be interpreted separately. In diagnostic procedures, standard Sanger type sequencing (mostly performed as a dye-dideoxynucleotide terminator system) is still the most commonly used method. This allows using established techniques for interpreting those types of genetic information. Besides reviewing the foundation of drug resistance interpretation for HBV, different interpretation systems, either commercially available (TRUGENE, Abbott, ViroScore) or free to use (geno2pheno[HBV], HIV-GRADE HBV tool), are compared in this article.
Clinicopathological Significance of microRNA-31, -143 and -145 Expression in Colorectal Cancer

We are just beginning to understand how microRNAs (miRNAs) are involved in tumor-related processes in humans. Applying real-time RT-PCR, we investigated the miR-31, miR-143 and miR-145 expression in 98 primary CRC specimens, along with the corresponding normal mucosa specimens, and analyze the relationship of their expression with clinicopathological features. Our results showed the miR-31 expression was up-regulated in CRC compared to normal mucosa (p = 0.001). Furthermore, miR-31 expression was positively related to advanced TNM stage (p = 0.026) and deeper invasion of tumors (p = 0.024). MiR-145 was down-regulated in both colon (p = 0.001) and rectal (p = 0.012) cancer. MiR-143 was only down-regulated in colon cancer (p = 0.023) but not in rectal cancer (p = 0.351). There was no relationship of miR-143 and miR-145 expression with other clinicopathological features (p > 0.05), except that the miR-145 expression was related to cancer site (p = 0.03). In conclusion, the miR-31 overexpression may be involved in the development and progression of CRC. The miR-143 and miR-145 may play a certain role in the development of colon and/or rectal cancers but not in progression of the disease.
Using virtual coordinates in the establishment of inter-domain LSPs

MultiProtocol Label Switching (MPLS) is used inside large ISP networks to provide services with stringent Service Level Agreements such as Virtual Private Networks (VPNs). Customers are now urging ISPs to provide such services across inter-domain boundaries. This requires the ability to establish inter-domain MPLS Label Switched Paths (LSPs) with constraints. Up to now, the literature has mostly focused on mechanisms to compute LSPs inside a single AS. In this paper, we propose two heuristics to select the downstream AS and the ingress router inside this AS for the establishment of inter-domain LSPs. Then, we evaluate them in terms of the quality of the resulting paths and the number of unsuccessful attempts.
Phylogeny and Molecular Identification of Vibrios on the Basis of Multilocus Sequence Analysis

ABSTRACT We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The families Vibrionaceae, Photobacteriaceae, Enterovibrionaceae, and Salinivibrionaceae were all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively. The genus Vibrio was heterogeneous and polyphyletic, with Vibrio fischeri, V. logei, and V. wodanis grouping closer to the Photobacterium genus. V. halioticoli-, V. harveyi-, V. splendidus-, and V. tubiashii-related species formed groups within the genus Vibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within the V. splendidus and V. tubiashii group, rpoA gene sequences were slightly less discriminatory than recA and pyrH sequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94% rpoA, recA, and pyrH gene sequence similarity, respectively.
Heterospecific pollen deposition in Delphinium barbeyi: linking stigmatic pollen loads to reproductive output in the field.

BACKGROUND AND AIMS Most pollinators are generalists and therefore are likely to transfer heterospecific pollen among co-flowering plants. Most work on the impacts of heterospecific pollen deposition on plant fecundity has utilized hand-pollination experiments in greenhouse settings, and we continue to know very little about the reproductive effects of heterospecific pollen in field settings. METHODS We explored how patterns of naturally deposited heterospecific pollen relate to the reproductive output of Delphinium barbeyi, a common subalpine perennial herb in the Rocky Mountains (USA). We assessed a wide range of naturally occurring heterospecific pollen proportions and pollen load sizes, and linked stigmatic pollen deposition directly to seed set in individual carpels in the field. KEY RESULTS We found that heterospecific pollen deposition in D. barbeyi is common, but typically found at low levels across stigmas collected in our sites. Neither conspecific nor heterospecific pollen deposition was related to carpel abortion. By contrast, we saw a significant positive relationship between conspecific pollen amount and viable seed production, as well as a significant negative interaction between the effects of conspecific pollen and heterospecific pollen amount, whereby the effect of conspecific pollen on viable seed production became weaker with greater heterospecific deposition on stigmas. CONCLUSIONS To our knowledge, this is the first demonstration of a relationship between heterospecific pollen and seed production in a field setting. In addition, it is the first report of an interaction between conspecific and heterospecific pollen quantities on seed production. These findings, taken with the results from other studies, suggest that greenhouse hand-pollination studies and field studies should be more tightly integrated in future work to better understand how heterospecific pollen transfer can be detrimental for plant reproduction.
Fetal Alcohol Exposure Impairs Alveolar Macrophage Function via Decreased Glutathione Availability

Immature function of the alveolar macrophage increases the risk of pulmonary infections in premature newborns. In utero alcohol increases fetal systemic oxidative stress. Because the premature lung is deficient in glutathione (GSH), we hypothesized that chronic in utero alcohol (ethanol) exposure exacerbates the oxidative stress within the developing lung, thereby impairing alveolar macrophage function. Additionally, we evaluated the effects of in vivo and in vitro GSH availability on ethanol-exposed macrophage function. Using a guinea pig model of chronic in utero ethanol exposure, fetal epithelial lining fluid (ELF) and alveolar macrophage GSH were decreased with increased markers of oxidative stress. Ethanol-exposed macrophage exhibited impaired phagocytosis and increased apoptosis compared with gestational control. When the GSH precursor S-adenosyl-methionine (SAM) was added to the maternal drinking water containing ethanol, fetal ELF and macrophage GSH were maintained and ELF oxidative stress diminished. In vivo maternal SAM therapy maintained macrophage phagocytosis and decreased apoptosis. In vitro GSH supplements also improved phagocytosis and viability in both premature and ethanol-exposed macrophage. This suggested that in utero ethanol impaired premature macrophage function and viability via decreased GSH availability. Furthermore, GSH supplementation during and after ethanol exposure improved fetal macrophage function and viability. These results add a new dimension to the detrimental effects of fetal alcohol exposure on the developing alveolar macrophage, raising the possibility of GSH therapy to augment premature alveolar macrophage function.
Pavilion Lake Microbialites: Morphological, Molecular and Biochemical Evidence for a Cold-Water Transition to Colonial Aggregates

The presence of microbialite structures in a freshwater, dimictic mid-latitude lake and their establishment after the last ice age about 10,000 years ago is puzzling. Freshwater calcite microbialites at Pavilion Lake, British Columbia, Canada, consist of a complex community of microorganisms that collectively form large, ordered structured aggregates. This distinctive assemblage of freshwater calcite microbialites was studied through standard microbial methods, morphological observations, phospholipid fatty acid (PLFA) analysis, DNA sequencing and the identification of quorum sensing molecules. Our results suggest that the microbialites may represent a transitional form from the exclusively prokaryotic colonial precursors of stromatolites to the multicellular organismic aggregates that give rise to coral reefs.
Isolation of Mycoplasma genitalium from First-Void Urine Specimens by Coculture with Vero Cells

ABSTRACT Isolation of Mycoplasma genitalium from clinical specimens remains difficult. We describe an improvement of the Vero cell coculture method in which the growth of M. genitalium was monitored by quantitative real-time PCR. Four new M. genitalium strains were isolated from six first-void urine specimens of male Japanese patients with urethritis. In two of them, only M. genitalium was detected: one also contained Ureaplasma urealyticum, and one contained Chlamydia trachomatis, Neisseria gonorrhoeae, U. urealyticum, and Ureaplasma parvum. In the specimens yielding isolates of M. genitalium, growth was documented by quantitative PCR after two to five passages in Vero cells. The complete isolation procedure from the initial inoculation to completion of single-colony cloning took about 1 year. Isolation of M. genitalium from urine specimens proved to be more difficult than from swab specimens. Due to the cytotoxic effect of urine, a procedure involving washing of the urinary sediment was introduced. Furthermore, prolonged storage of the urine specimens before culture was shown to be detrimental to the success of isolation, as shown by the lack of success in attempts to isolate M. genitalium from mailed urine specimens as well as by simulation experiments. High concentrations of penicillin G and amphotericin B were surprisingly inhibitory to the growth of wild-type M. genitalium strains, but penicillin G at 200 IU/ml and polymyxin B at 500 μg/ml could be used as selective antibiotics to avoid bacterial overgrowth in the Vero cell cultures.
Defective collagen-induced platelet activation in two patients with malignant haemopathies is related to a defect in the GPVI-coupled signalling pathway

Summary The occurrence of a thrombocytopathy concomitantly to the development of a malignant haemopathy has been reported for some time, but little is known about the mechanism(s) involved in the platelet dysfunction. Platelet glycoprotein VI (GPVI) has now been identified as a principal platelet receptor for collagen. In this paper, we report the cases of two patients with a myelodysplasia and a B lymphopathy, respectively, who presented with thrombocytopathy in relation to a defective GPVI-mediated platelet reactivity to collagen. Thus, with regard to the different steps of adhesion, activation secretion or aggregation, patients’ platelet responses to collagen and to the GPVI specific agonists, collagen related peptide (CRP) or convulxin were null or dramatically impaired. Platelet responses to other agonists ADP, TRAP,Arachidonic acid were normal or showed only a moderate decrease. GPVI content was repeatedly normal, and binding of specific ligands, such as convulxin, satisfactory. Nevertheless, specific activating monoclonal antibodies and convulxin failed to induce platelet secretion; collagen, CRP or convulxin were unable to provoke calcium mobilisation. Furthermore, using a perfusion chamber model, we showed that ex vivo collagen-induced thrombi formation was very impaired.Taken together,these data provide evidence, for the first time, of an acquired defect in GPVI-mediated platelet reactivity to collagen, which reflects data observed in constitutional GPVI deficiencies, in two patients with malignant haemopathies.
Segmented shape-symbolic time series representation

This paper introduces a symbolic time series representation using monotonic sub-sequences and bottom up segmentation. The representation min- imizes the square error between the segments and their monotonic approximations. The representation can robustly classify the direction of a segment and is scale in- variant with respect to the time and value dimensions. This paper describes two experiments. The first shows how accurately the monotonic functions are able to discriminate between different segments. The second tests how well the segmenta- tion technique recognizes segments and classifies them with correct symbols. Fi- nally this paper illustrates the new representation on real-world data.
Informing efficient randomised controlled trials: exploration of challenges in developing progression criteria for internal pilot studies

Objectives Designing studies with an internal pilot phase may optimise the use of pilot work to inform more efficient randomised controlled trials (RCTs). Careful selection of preagreed decision or ‘progression’ criteria at the juncture between the internal pilot and main trial phases provides a valuable opportunity to evaluate the likely success of the main trial and optimise its design or, if necessary, to make the decision not to proceed with the main trial. Guidance on the appropriate selection and application of progression criteria is, however, lacking. This paper outlines the key issues to consider in the optimal development and review of operational progression criteria for RCTs with an internal pilot phase. Design A structured literature review and exploration of stakeholders' opinions at a Medical Research Council (MRC) Hubs for Trials Methodology Research workshop. Key stakeholders included triallists, methodologists, statisticians and funders. Results There is considerable variation in the use of progression criteria for RCTs with an internal pilot phase, although 3 common issues predominate: trial recruitment, protocol adherence and outcome data. Detailed and systematic reporting around the decision-making process for stopping, amending or proceeding to a main trial is uncommon, which may hamper understanding in the research community about the appropriate and optimal use of RCTs with an internal pilot phase. 10 top tips for the development, use and reporting of progression criteria for internal pilot studies are presented. Conclusions Systematic and transparent reporting of the design, results and evaluation of internal pilot trials in the literature should be encouraged in order to facilitate understanding in the research community and to inform future trials.
Geo-Biological Coupling of Authigenic Carbonate Formation and Autotrophic Faunal Colonization at Deep-Sea Methane Seeps I: Geo-Biological Settings

Methane (CH4) in sub-seafloor sediment is generated both biologically and non-biologically from organic and inorganic sources. A major part of the sub-seafloor methane is oxidized before leakage via “anaerobic oxidation of methane” (AOM) in the subsurface. The AOM-survivor methane, which is relatively minor part of the subsurface methane, leaches to the overlying water column and is eventually subject to thorough anaerobic and aerobic oxidation in the water column. The AOM with sulfate results in the generation of carbon dioxide and sulfide; the former (CO2) is incorporated into authigenic carbonate and autotrophic biomass, and the autotrophy is energetically driven by oxidation of the latter (H2S). These processes are typically observed at focused sites that are generally known as “methane seeps” or hydrocarbon seeps, or occasionally called as cold seeps in comparison with hydrothermal vents. Methane seeps are typically formed in passive and active continental margins, occasionally with unique features such as exposed methane hydrates, mud volcanoes, asphalt volcanoes, salt diapirs, and brine pools. Accordingly, authigenic carbonates and unique biological communities are shaped at respective methane seeps. This chapter overviews geological and biological setting for the formation of methane seeps associated with unique landscapes of carbonates and biomes.