Miracle-dz/UniFAR-FTUs huggingface dataset:
Short-term disturbance by a commercial two-dimensional seismic survey does not lead to long-term displacement of harbour porpoises

Assessments of the impact of offshore energy developments are constrained because it is not known whether fine-scale behavioural responses to noise lead to broader-scale displacement of protected small cetaceans. We used passive acoustic monitoring and digital aerial surveys to study changes in the occurrence of harbour porpoises across a 2000 km2 study area during a commercial two-dimensional seismic survey in the North Sea. Acoustic and visual data provided evidence of group responses to airgun noise from the 470 cu inch array over ranges of 5–10 km, at received peak-to-peak sound pressure levels of 165–172 dB re 1 µPa and sound exposure levels (SELs) of 145–151 dB re 1 µPa2 s−1. However, animals were typically detected again at affected sites within a few hours, and the level of response declined through the 10 day survey. Overall, acoustic detections decreased significantly during the survey period in the impact area compared with a control area, but this effect was small in relation to natural variation. These results demonstrate that prolonged seismic survey noise did not lead to broader-scale displacement into suboptimal or higher-risk habitats, and suggest that impact assessments should focus on sublethal effects resulting from changes in foraging performance of animals within affected sites.
Comparing visual features for lipreading

For automatic lipreading, there are many competing methods for feature extraction. Often, because of the complexity of the task these methods are tested on only quite restricted datasets, such as the letters of the alphabet or digits, and from only a few speakers. In this paper we compare some of the leading methods for lip feature extraction and compare them on the GRID dataset which uses a constrained vocabulary over, in this case, 15 speakers. Previously the GRID data has had restricted attention because of the requirements to track the face and lips accurately. We overcome this via the use of a novel linear predictor (LP) tracker which we use to control an Active Appearance Model (AAM). By ignoring shape and/or appearance parameters from the AAM we can quantify the effect of appearance and/or shape when lip-reading. We find that shape alone is a useful cue for lipreading (which is consistent with human experiments). However, the incremental effect of shape on appearance appears to be not significant which implies that the inner appearance of the mouth contains more information than the shape.
Nab-Paclitaxel Plus S-1 Shows Increased Antitumor Activity in Patient-Derived Pancreatic Cancer Xenograft Mouse Models

Objectives To investigate the antitumor activity of nanoparticle albumin-bound paclitaxel (nab-paclitaxel) plus S-1 in patient-derived pancreatic cancer xenograft mouse models and to explore biomarkers that could predict drug efficacy. Methods Ten patient-derived xenograft models were established. The third-generation tumor-bearing mice were randomized into 4 treatment groups: (1) control; (2) S-1; (3) nab-paclitaxel; (4) S-1 plus nab-paclitaxel. Resected tumors were tested by immunohistochemistry for the expression of thymidylate synthase, orotate phosphoribosyltransferase (OPRT), dihydropyrimidine dehydrogenase (DPD), secreted protein that is acidic and rich in cysteine, human epidermal growth factor receptor 2 (HER2), collagen-1, and CD31. Results Tumor growth inhibition of the S-1 group, nab-paclitaxel group, and combination group was 69.52%, 86.63%, 103.56%, respectively (P < 0.05). The efficacy of S-1 is better in thymidylate synthase–negative, OPRT-positive, and DPD-negative tumors. The efficacy of nab-paclitaxel is better in HER2-positive tumors. Collagen-1 was decreased and CD31 was increased in tumors treated with nab-paclitaxel and S-1 plus nab-paclitaxel compared with control or S-1. Conclusions This preclinical study showed that S-1 plus nab-paclitaxel exerted significantly better antitumor activity than S-1 or nab-paclitaxel alone. Thymidylate synthase, OPRT, and DPD were possibly biomarkers of S-1 and HER2 of nab-paclitaxel.
Indirect Effects of Conservation Policies on the Coupled Human-Natural Ecosystem of the Upper Gulf of California

High bycatch of non-target species and species of conservation concern often drives the implementation of fisheries policies. However, species- or fishery-specific policies may lead to indirect consequences, positive or negative, for other species or fisheries. We use an Atlantis ecosystem model of the Northern Gulf of California to evaluate the effects of fisheries policies directed at reducing bycatch of vaquita (Phocoena sinus) on other species of conservation concern, priority target species, and metrics of ecosystem function and structure. Vaquita, a Critically Endangered porpoise endemic to the Upper Gulf of California, are frequently entangled by finfish gillnets and shrimp driftnets. We tested five fishery management scenarios, projected over 30 years (2008 to 2038), directed at vaquita conservation. The scenarios consider progressively larger spatial restrictions for finfish gillnets and shrimp driftnets. The most restrictive scenario resulted in the highest biomass of species of conservation concern; the scenario without any conservation measures in place resulted in the lowest. Vaquita experienced the largest population increase of any functional group; their biomass increased 2.7 times relative to initial (2008) levels under the most restrictive spatial closure scenario. Bycatch of sea lions, sea turtles, and totoaba decreased > 80% in shrimp driftnets and at least 20% in finfish gillnet fleets under spatial management. We found indirect effects on species and ecosystem function and structure as a result of vaquita management actions. Biomass and catch of forage fish declined, which could affect lower-trophic level fisheries, while other species such as skates, rays, and sharks increased in both biomass and catch. When comparing across performance metrics, we found that scenarios that increased ecosystem function and structure resulted in lower economic performance indicators, underscoring the need for management actions that consider ecological and economic tradeoffs as part of the integrated management of the Upper Gulf of California.
Evaluation of sodium hypochlorite as a denture cleanser: a clinical study.

OBJECTIVES To evaluate the effect of sodium hypochlorite (NaOCl) on biofilms, colour stability (ΔE) and surface roughness (Ra) of complete dentures and patient acceptability. BACKGROUND Denture cleansers should be able to reduce the accumulation of biofilms without affecting the acrylic resin properties. Patient satisfaction is important to maintaining their daily use. MATERIALS AND METHODS Fifteen participants were instructed to keep their dentures immersed daily in a 0.5% NaOCl solution for 3 min over 90 days. Swabs were taken from dentures and inoculated on CHROMagar and blood agar. The number of colony-forming units (cfu) was counted after a 48-h incubation period. ΔE was assessed using the CIE L*a*b* system. Ra was measured using a profilometer. Patient acceptability was checked based on their degree of satisfaction. Cell counts, ΔE and Ra were analysed using anova, Friedman's and Kruskal-Wallis tests, respectively (α = 0.05). RESULTS A significant reduction in the total number of microorganisms (p = 0.001) and Candida spp. was noticed. No significant differences were found for ΔE (p = 0.68) and for Ra (p = 0.47). The level of the patient satisfaction increased throughout the follow-up period. CONCLUSION The 0.5% NaOCl solution was effective in reducing microorganisms without significant changes in colour or roughness of denture resin. The participants reported satisfaction with the cleaning results.
The Efficacy of a Haptic-Enhanced Virtual Reality System for Precision Grasp Acquisition in Stroke Rehabilitation

Stroke is a leading cause of long-term disability, and virtual reality- (VR-) based stroke rehabilitation is effective in increasing motivation and the functional performance. Although much of the functional reach and grasp capabilities of the upper extremities were regained, the pinch movement remains impaired following stroke. In this study, we developed a haptic-enhanced VR system to simulate haptic pinch tasks to assist the recovery of upper-extremity fine motor function. We recruited 16 adults with stroke to verify the efficacy of this new VR system. Each patient received 30 min VR training sessions 3 times per week for 8 weeks. Outcome measures, Fugl-Meyer assessment (FMA), Test Evaluant les Membres superieurs des Personnes Agees (TEMPA), Wolf motor function test (WMFT), Box and Block test (BBT), and Jamar grip dynamometer, showed statistically significant progress from pretest to posttest and follow-up, indicating that the proposed system effectively promoted fine motor recovery of function. Additionally, our evidence suggests that this system was also effective under certain challenging conditions such as being in the chronic stroke phase or a coside of lesion and dominant hand (nondominant hand impaired). System usability assessment indicated that the participants strongly intended to continue using this VR-based system in rehabilitation.
Papillary microcarcinoma of the thyroid gland: Is the immunohistochemical expression of cyclin D1 or galectin-3 in primary tumour an indicator of metastatic disease?

Introduction. Papillary microcarcinomas (PMC) of the thyroid gland are defined according to The WHO Committee as papillary carcinomas measuring 10 mm or less in diameter. A large proportion of these tumours are found coincidentally in the treatment of symptomatic goitre and most cases follow an indolent course with an excellent prognosis. However, a more aggressive behaviour with regional and distant metastases does occur. The aim of this study was to evaluate if the immunohistochemical markers cyclin D1 or galectin-3 might indicate the presence of metastatic disease in patients with PMC at the time of diagnosis. Material and methods. From the 1st of January 1996 to 31st of December 2002 a total of 169 PMC patients were diagnosed and registered in the national Danish thyroid cancer database DATHYRCA and 131 of these were eligible for the study. Forty-three (33%) had histologically verified regional or distant metastases. Slides were cut from the primary tumour and immunostaining and quantification was subsequently performed. Results. The percentage of positive cells was examined for patients with and without metastases. For cyclin D1 the median values were 31% (range: 0–59) and 21% (range: 0–75), respectively, showing a statistically significant difference (p=0.02). For galectin-3 the medians were 87% (range: 6–96) and 85% (range: 0–99) and no significant difference was found. Conclusion. Cyclin D1 showed significantly higher median expression in patients with metastases compared to those without, indicating a correlation to tumour aggressiveness. However, both groups showed large variation in expression, which disqualify the marker as a discriminator for the detection of metastases. Galectin-3 was without any significant correlation to the presence of metastases from PMC.
Does the Effect of PM10 on Mortality Depend on PM Nickel and Vanadium Content? A Reanalysis of the NMMAPS Data

Background Lack of knowledge regarding particulate matter (PM) characteristics associated with toxicity is a crucial research gap. Short-term effects of PM can vary by location, possibly reflecting regional differences in mixtures. A report by Lippmann et al. [Lippmann et al., Environ Health Perspect 114:1662–1669 (2006)] analyzed mortality effect estimates from the National Morbidity, Mortality, and Air Pollution Study (NMMAPS) for 1987–1994. They found that average concentrations of nickel or vanadium in PM2.5 (PM with aerodynamic diameter < 2.5 μm) positively modified the lag-1 day association between PM10 and all-cause mortality. Objective We reestimated the relationship between county-specific lag-1 PM10 (PM with aerodynamic diameter < 10 μm) effects on mortality and county-specific nickel or vanadium PM2.5 average concentrations using 1987–2000 effect estimates. We explored whether such modification is sensitive to outliers. Methods We estimated long-term average county-level nickel and vanadium PM2.5 concentrations for 2000–2005 for 72 U.S. counties representing 69 communities. We fitted Bayesian hierarchical regression models to investigate whether county-specific short-term effects of PM10 on mortality are modified by long-term county-specific nickel or vanadium PM2.5 concentrations. We conducted sensitivity analyses by excluding individual communities and considering log-transformed data. Results Our results were consistent with those of Lippmann et al. However, we found that when counties included in the NMMAPS New York community were excluded from the sensitivity analysis, the evidence of effect modification of nickel or vanadium on the short-term effects of PM10 mortality was much weaker and no longer statistically significant. Conclusions Our analysis does not contradict the hypothesis that nickel or vanadium may increase the risk of PM to human health, but it highlights the sensitivity of findings to particularly influential observations.
The Safety and Acceptance of the PrePex Device for Non-Surgical Adult Male Circumcision in Rakai, Uganda. A Non-Randomized Observational Study

Objectives To assess the safety and acceptance of the PrePex device for medical male circumcision (MMC) in rural Uganda. Methods In an observational study, HIV-uninfected, uncircumcised men aged 18 and older who requested elective MMC were informed about the PrePex and dorsal slit methods and offered a free choice of their preferred procedure. 100 men received PrePex to assess preliminary safety (aim 1). An additional 329 men, 250 chose PrePex and 79 chose Dorsal slit, were enrolled following approval by the Safety Monitoring Committee (aim 2). Men were followed up at 7 days to assess adverse events (AEs) and to remove the PrePex device. Wound healing was assessed at 4 weeks, with subsequent weekly follow up until completed healing. Results The PrePex device was contraindicated in 5.7% of men due to a tight prepuce or phimosis/adhesions. Among 429 enrolled men 350 (82.0%) got the PrePex device and 79 (18.0%) the dorsal slit procedure. 250 of 329 men (76.0%) who were invited to choose between the 2 procedures chose Prepex. There were 9 AEs (2.6%) with the PrePex, of which 5 (1.4%) were severe complications, 4 due to patient self-removal of the device leading to edema and urinary obstruction requiring emergency surgical circumcision, and one due to wound dehiscence following device removal. 71.8% of men reported an unpleasant odor prior to PrePex removal. Cumulative rates of completed wound healing with the PrePex were 56.7% at week 4, 84.8% week 5, 97.6% week 6 and 98.6% week 7, compared to 98.7% at week 4 with dorsal slit (p<0.0001). Conclusion The PrePex device was well accepted, but healing was slower than with dorsal slit surgery. Severe complications, primarily following PrePex self-removal, required rapid access to emergency surgical facilities. The need to return for removal and delayed healing may increase Program cost and client burden.
Characterization of Glioma Microcirculation and Tissue Features Using Intravoxel Incoherent Motion Magnetic Resonance Imaging in a Rat Brain Model

PurposeOur aim was to investigate the pertinence of diffusion and perfusion magnetic resonance imaging (MRI) parameters obtained at 17.2 T in a 9L glioma rat brain tumor model to evaluate tumor tissue characteristics. Materials and MethodsThe local animal ethics advisory committee approved this study. 9L glioma cells were injected intracerebrally to 14 Fischer rats. The animals were imaged at 7 or 12 days after implantation on a 17.2-T MRI scanner, using 72 different b values (2–3025 s/mm2). The signal attenuation, S/So, was fitted using a kurtosis diffusion model (ADCo and K) and a biexponential diffusion model (fractions ffast and fslow and diffusion coefficients Dfast and Dslow) using b values greater than 300 s/mm2. To bridge the 2 models, an average diffusion coefficient and a biexponential index were estimated from the biexponential model as ADCo and K equivalents, respectively. Intravoxel incoherent motion perfusion–related parameters were obtained from the residual signal at low b values, after the diffusion component has been removed. Diffusion and perfusion maps were generated for each fitted parameter on a pixel-by-pixel basis, and regions of interest were drawn in the tumor and contralateral side to retrieve diffusion and perfusion parameters. All rats were killed and cellularity and vascularity were quantitatively assessed using histology for comparison with diffusion and perfusion parameters. ResultsIntravoxel incoherent motion maps clearly highlighted tumor areas as generally heterogeneous, as confirmed by histology. For diffusion parameters, ADCo and were not significantly different between the tumor and contralateral side, whereas K in the tumor was significantly higher than in contralateral basal ganglia (P < 0.0001), as well as biexponential index (P < 0.001). ADCo and in the tumor at day 7 were significantly higher than at day 12 (P < 0.01 and P < 0.001, respectively). fIVIM in the tumor from the kurtosis diffusion model was significantly higher than in contralateral basal ganglia (P < 0.001). fIVIM in the tumor at day 7 was significantly higher than in the tumor at day 12 (P < 0.0001). There was no significant difference for D* between the tumor and contralateral side (P = 0.06). A significant negative correlation was found between tumor vascularity and fIVIM (P < 0.05) as well as between tumor cell count and (P < 0.01). ConclusionQuantitative non-Gaussian diffusion and perfusion MRI can provide valuable information on microvasculature and tissue structure to improve characterization of brain tumors.
Expression and Regulation of the Endogenous Retrovirus 3 in Hodgkin’s Lymphoma Cells

Human endogenous retroviruses (ERV) are an integral part of our genome. Expression of ERV is usually switched off but reactivation of ERV has been observed in varying human diseases including cancer. Recently, reactivation of ERV associated promoters in Hodgkin’s lymphoma (HL) cells has been described. Despite relatively good prognosis, not all patients with HL can be cured with the established therapy and this therapy is associated with severe late side effects. Therefore, new targets are required for the development of future treatment strategies. Reactivated ERV might represent such target structures. Therefore, we asked which ERV loci are expressed in HL cells. Using DNA microarray analysis, we found no evidence for a general activation of ERV transcription in HL cells. In contrast, we observed down-regulation of ERV3, an ERV with potential tumor suppressor function, in HL cells in comparison to normal blood cells. Interestingly, ERV3 was also differentially expressed in published DNA microarray data from resting versus cycling B cells. Treatment of HL cells with the histone deacetylase inhibitor vorinostat strongly up-regulated ERV3 expression. In addition, we observed up-regulation in HL cells after treatment with hypoxia-mimetic cobalt(II) chloride. Like vorinostat, cobalt(II) chloride inhibited cell growth of HL cells. Our results suggest that cell cycle inhibition of HL cells is accompanied by up-regulation of ERV3.
Centers of Monotone Generalized Complementarity Problems

Let C be a full dimensional, closed, pointed and convex cone in a finite dimensional real vector space E with an inner product of x, y ∈ E, and M a maximal monotone subset of E × E. This paper studies the existence and continuity of centers of the monotone generalized complementarity problem associated with C and M: Find x, y ∈ M ∩ C × C* such that = 0. Here C* = {y ∈ E : ≥ 0 for all x ∈ C} denotes the dual cone of C. The main result of the paper unifies and extends some results established for monotone complementarity problems in Euclidean space and monotone semidefinite linear complementarity problems in symmetric matrices.
Electrotransformation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis with Various Plasmids

ABSTRACT We describe, for the first time, a detailed electroporation procedure for Lactobacillus delbrueckii. Three L. delbrueckii strains were successfully transformed. Under optimal conditions, the transformation efficiency was 104 transformants per μg of DNA. Using this procedure, we identified several plasmids able to replicate in L. delbrueckii and integrated an integrative vector based on phage integrative elements into the L. delbrueckii subsp. bulgaricus chromosome. These vectors provide a good basis for developing molecular tools for L. delbrueckii and open the field of genetic studies in L. delbrueckii.
MORC2 mutation causes severe spinal muscular atrophy-phenotype, cerebellar atrophy, and diaphragmatic paralysis.

Sir, With great interest, we read the article by Sevilla et al. (2016) delineating mutations in MORC 2 as a novel genetic cause for axonal Charcot-Marie-Tooth (CMT) disease type 2Z (OMIM #616688) with dominant inheritance. The authors detected MORC2 mutations in nine patients from three unrelated families and showed MORC2 to be expressed in both axons and Schwann cells of the peripheral nerve (Sevilla et al. , 2016). MORC2 belongs to the group of highly conserved MORC proteins, which all share CW-zinc finger and GHL (Gyrase B-Hsp90-MutL)-ATPase domains (Li et al. , 2013). MORC2 is predominantly expressed in the nucleus and is supposed to be relevant for chromatin remodelling, DNA-repair, transcriptional regulation, and lipid metabolism (Shao et al. , 2010; Li et al. , 2012). Following publications describing seven mutations underline the importance of this gene as a novel cause for CMT (Albulym et al. , 2016; Hyun et al. , 2016; Lassuthova et al. , 2016; Zhao et al. , 2016). Following this publication, we re-examined whole exome and whole genome sequencing data of a cohort of 32 patients from 23 families with genetically unsolved neuropathies for mutations in MORC2 and identified a novel de novo c.1085C>G (p.T362R) MORC2 mutation. The 5-year-old girl did not show a CMT phenotype but suffered from severe spinal muscular atrophy (SMA)-like disease with neuropathy, cerebellar atrophy, and diaphragmatic paralysis. This observation broadens the phenotypical spectrum of MORC2 -related disorders towards SMA, spinal muscular atrophy with respiratory distress type 1 (SMARD1), and pontocerebellar hypoplasia. The study was approved by the institutional review board of the Charite (EA1/222/08). Parents provided written informed consent for all aspects of the study according to the Declaration of Helsinki. The now …