Miracle-dz/UniFAR-FTUs huggingface dataset:
Chest CT scan findings in World Trade Center workers

ABSTRACT We examined the chest CT scans of 1,453 WTC responders using the International Classification of High-resolution CT for Occupational and Environmental Respiratory Diseases. Univariate and bivariate analyses of potential work-related pleural abnormalities were performed with pre-WTC and WTC-related occupational exposure data, spirometry, demographics and quantitative CT measurements. Logistic regression was used to evaluate occupational predictors of those abnormalities. Chest CT scans were performed first at a median of 6.8 years after 9/11/2001. Pleural abnormalities were the most frequent (21.1%) across all occupational groups In multivariable analyses, significant pre-WTC occupational asbestos exposure, and work as laborer/cleaner were predictive of pleural abnormalities, with prevalence being highest for the Polish subgroup (n = 237) of our population. Continued occupational lung disease surveillance is warranted in this cohort.
Acute vitreoretinal trauma and inflammation after traumatic brain injury in mice

Limited attention has been given to ocular injuries associated with traumatic brain injury (TBI). The retina is an extension of the central nervous system and evaluation of ocular damage may offer a less‐invasive approach to gauge TBI severity and response to treatment. We aim to characterize acute changes in the mouse eye after exposure to two different models of TBI to assess the utility of eye damage as a surrogate to brain injury.
Combined effects of starvation and butyrate on autophagy‐dependent gingival epithelial cell death

BACKGROUND AND OBJECTIVE Bacteria in the dental biofilm surrounding marginal gingival grooves cause periodontal diseases. Numerous bacteria within the biofilm consume nutrients from the gingival crevicular fluid. Furthermore, some gram-negative bacteria in mature dental biofilms produce butyrate. Thus, gingival epithelial cells in close proximity to mature dental biofilms are at risk of both starvation and exposure to butyrate. In the present study, we determined the combined effects of starvation and butyrate exposure on gingival epithelial cell death and the underlying mechanisms. MATERIAL AND METHODS The Ca9-22 cell line was used as an in vitro counterpart of gingival epithelial cells. Cell death was measured as the amount of total DNA in the dead cells using SYTOX Green dye, which penetrates through membranes of dead cells and emits fluorescence when it intercalates into double-stranded DNA. AMP-activated protein kinase (AMPK) activity, the amount of autophagy, and acetylation of histone H3 were determined using western blot. Gene expression levels of microtubule-associated protein 1 light chain 3b (lc3b) were determined using quantitative reverse transcription-polymerase chain reaction. RESULTS Butyrate-induced cell death occurred in a dose-dependent manner whether cells were starved or fed. However, the induction of cell death was two to four times higher when cells were placed under starvation conditions compared to when they were fed. Moreover, both starvation and butyrate exposure induced AMPK activity and autophagy. While AMPK inactivation resulted in decreased autophagy and butyrate-induced cell death under conditions of starvation, AMPK activation resulted in butyrate-induced cell death when cells were fed. Combined with the results of our previous report, which demonstrated butyrate-induced autophagy-dependent cell death, the results of this study suggest that the combination of starvation and butyrate exposure activates AMPK inducing autophagy and subsequent cell death. Notably, this combination markedly induced LC3B production and the induction was attenuated by AMPK inhibition. LC3B knockdown, in turn, significantly decreased butyrate-induced cell death. Therefore, AMPK-dependent LC3B induction apparently plays an important role in butyrate-induced cell death. There was a lack of correspondence between the levels of AMPK activation and LC3B induction; this may reflect the histone deacetylase-inhibitory capacity of butyrate on histone proteins. CONCLUSION Taken together, starvation and butyrate exposure promote autophagy via AMPK signaling, while the histone deacetylase-inhibitory effects of butyrate alter chromatin to transcriptionally active state, resulting in strong LC3B induction and subsequent cell death. These findings may help improve the understanding of the cellular processes underlying periodontal disease initiation.
Identi ﬁ cation and Characterization of Small Molecules That Inhibit Nonsense-Mediated RNA Decay and Suppress Nonsense p53 Mutations

Many of the gene mutations found in genetic disorders, including cancer, result in premature termination codons(PTC)andtherapiddegradationoftheirmRNAsbynonsense-mediatedRNAdecay(NMD). Weusedvirtual library screening, targeting a pocket in the SMG7 protein, a key component of the NMD mechanism, to identify compounds that disrupt the SMG7 – UPF1 complex and inhibit NMD. Several of these compounds upregulated NMD-targeted mRNAs at nanomolar concentrations, with minimal toxicity in cell-based assays. As expected, pharmacologic NMD inhibition disrupted SMG7 – UPF1 interactions. When used in cells with PTC-mutated p53, pharmacologic NMD inhibition combined with a PTC "read-through" drug led to restoration of full-length p53 protein, upregulation of p53 downstream transcripts, and cell death. These studies serve as proof-of-concept that pharmacologic NMD inhibitors can restore mRNA integrity in the presence of PTC and can be used as part of a strategy to restore full-length protein in a variety of genetic diseases. Cancer Res; 74(11); 1 – 10. (cid:1) 2014 AACR.
Genomics and cure: understanding narratives of patients with Duchenne muscular dystrophy in Japan

ABSTRACT Globally, genomics research is expected to enhance the health of patients with intractable diseases such as Duchenne muscular dystrophy (DMD). But how do patients perceive medical and scientific attempts at creating drugs and finding cure, and why? Since the 1990s, a number of clinical trials for patients of DMD have been organized. Among them are a gene therapy and exon skipping, and they indicate the possibility of finding therapies for DMD patients. Since 2011, Japanese medical institutions have been participating in Global Clinical Trials so that Japanese DMD patients can have access to them once developed. Despite ongoing global clinical trials, however, field research shows that the DMD patients the author encountered were neither enthusiastic nor well informed about gene therapies developed in Japan or elsewhere. Why not? The author observed that the desire for a cure among DMD patients is not self-evident, but is framed by sociocultural conditions surrounding the patients, the local history of discrimination against genetic disorders, and the way care is organised. These factors further interplay with physical and mental conditions particular to DMD, affecting patients’ desire for a cure. This paper discusses the perception of genomics research and the possibility of a cure of DMD patients the author encountered in Japan, indicating that such perceptions are a result of the deeply-related interactions of the conditions in which patients live. Finally, the author suggests how commonly held views of patients and patients’ desire for cure need to be nuanced in genomic medicine. Data in this paper were collected between April and July 2014, and between 1996 and 2005 in Japan.
Prediction and analysis of ductile fracture in sheet metal forming—Part I: A modified Ayada criterion

A modified ductile fracture criterion is proposed based on the traditional Ayada criterion and coded into the finite element simulation platform of VUMAT/ABAQUS for prediction and analysis of ductile fracture in metal plastic strain processes. In this modified ductile fracture criterion, stress triaxiality is taken into account, and more importantly, the exponential effect of the equivalent plastic strain on the damage behavior, which is generally ignored in other ductile fracture criteria, is also considered. The material related constants in the modified ductile fracture criterion are determined by tensile tests together with finite element simulations. The applicability and reliability of the ductile fracture criterion in ductile fracture prediction in two types of classic stress states, viz. shear stress, tensile stress in sheet metal forming, are investigated based on the deformation behavior and fracture occurrence in two case studies with two typical types of materials, i.e. Al 6061 and T10A. The materials have a wide range of plasticity. The simulation and experimental results verify the applicability and reliability of the developed ductile fracture criterion in prediction of the ductile fracture with and without necking in different stress states of plastic strain.
Biomechanical differences in the weightlifting snatch between successful and unsuccessful lifts

The purpose of this study was to determine what differences exist between several kinematic variables between failed and successful attempts in the snatch lift. Six female Weightlifters at the 2015 American open were measured for kinematic variables via videotape during competition. The results show that differences existed in the angle of the shoulder at peak barbell height and the catch height, along with the amount of separation between the lifter and barbell at peak height. Significant differences were also found at the angle between the barbell and lifter center of mass. This study was a first step toward understanding the importance of the lifter’s ability to quickly and accurately pull themselves under the barbell. A better understanding of this association may help to improve coaches’ abilities to develop drills to improve consistency in barbell path. BIOMECHANICAL DIFFERENCES IN THE WEIGHTLIFTING SNATCH BETWEEN SUCCESSFUL AND UNSUCCESSFUL LIFTS A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree Master of Arts
An Activated Form of UFO Alters Leaf Development and Produces Ectopic Floral and Inflorescence Meristems

Plants are unique in their ability to continuously produce new meristems and organ primordia. In Arabidopsis, the transcription factor LEAFY (LFY) functions as a master regulator of a gene network that is important for floral meristem and organ specification. UNUSUAL FLORAL ORGANS (UFO) is a co-activator of LEAFY and is required for proper activation of APETALA3 in the floral meristem during the specification of stamens and petals. The ufo mutants display defects in other parts of the flower and the inflorescence, suggestive of additional roles. Here we show that the normal determinacy of the developing Arabidopsis leaves is affected by the expression of a gain-of-function UFO fusion protein with the VP16 transcriptional activator domain. In these lines, the rosette and cauline leaf primordia exhibit reiterated serration, and upon flowering produce ectopic meristems that develop into flowers, bract leaves and inflorescences. These striking phenotypes reveal that developing leaves maintain the competency to initiate flower and inflorescence programs. Furthermore, the gain-of-function phenotypes are dependent on LFY and the SEPALLATA (SEP) MADS-box transcription factors, indicative of their functional interactions with UFO. The findings of this study also suggest that UFO promotes the establishment of the lateral meristems and primordia in the peripheral zone of the apical and floral meristems by enhancing the activity of LFY. These novel phenotypes along with the mutant phenotypes of UFO orthologs in other plant species suggest a broader function for UFO in plants.
Assessing the disturbance potential of small unoccupied aircraft systems (UAS) on gray seals (Halichoerus grypus) at breeding colonies in Nova Scotia, Canada

The use of small unoccupied aircraft systems (UAS) for ecological studies and wildlife population assessments is increasing. These methods can provide significant benefits in terms of costs and reductions in human risk, but little is known if UAS-based approaches cause disturbance of animals during operations. To address this knowledge gap, we conducted a series of UAS flights at gray seal breeding colonies on Hay and Saddle Islands in Nova Scotia, Canada. Using a small fixed-wing UAS, we assessed both immediate and short-term effects of surveys using sequential image analysis and between-flight seal counts in ten, 50 m2 random quadrats at each colony. Counts of adult gray seals and young-of-the-year animals between first and second flights revealed no changes in abundance in quadrats (matched pair t-test p > 0.69) and slopes approaching 1 for linear regression comparisons (r2 > 0.80). Sequential image analysis revealed no changes in orientation or posture of imaged animals. We also assessed the acoustic properties of the small UAS in relation to low ambient noise conditions using sound equivalent level (Leq) measurements with a calibrated U-MIK 1 and a 1/3 octave band soundscape approach. The results of Leq measurements indicate that small fixed-wing UAS are quiet, with most energy above 160 Hz, and that levels across 1/3 octave bands do not greatly exceed ambient acoustic measurements in a quiet field during operations at standard survey altitudes. As such, this platform is unlikely to acoustically disturb gray seals at breeding colonies during population surveys. The results of the present study indicate that the effects of small fixed-wing UAS on gray seals at breeding colonies are negligible, and that fixed-wing UAS-based approaches should be considered amongst best practices for assessing gray seal colonies.
Pol-SARAS: A Fully Polarimetric SAR Raw Signal Simulator for Extended Soil Surfaces

We present a new synthetic aperture radar (SAR) raw signal simulator, which is able to simultaneously generate raw signals of different polarimetric channels of a polarimetric SAR system in such a way that a correct covariance matrix is obtained for the final images. Extended natural scenes, dominated by surface scattering, are considered. A fast Fourier-domain approach is used for the generation of raw signals. Presentation of theory is supplemented by meaningful experimental results, including a comparison of simulations with real polarimetric scattering data.
The Not4 E3 Ligase and CCR4 Deadenylase Play Distinct Roles in Protein Quality Control

Eukaryotic cells control their proteome by regulating protein production and protein clearance. Protein production is determined to a large extent by mRNA levels, whereas protein degradation depends mostly upon the proteasome. Dysfunction of the proteasome leads to the accumulation of non-functional proteins that can aggregate, be toxic for the cell, and, in extreme cases, lead to cell death. mRNA levels are controlled by their rates of synthesis and degradation. Recent evidence indicates that these rates have oppositely co-evolved to ensure appropriate mRNA levels. This opposite co-evolution has been correlated with the mutations in the Ccr4-Not complex. Consistently, the deadenylation enzymes responsible for the rate-limiting step in eukaryotic mRNA degradation, Caf1 and Ccr4, are subunits of the Ccr4-Not complex. Another subunit of this complex is a RING E3 ligase, Not4. It is essential for cellular protein solubility and has been proposed to be involved in co-translational quality control. An open question has been whether this role of Not4 resides strictly in the regulation of the deadenylation module of the Ccr4-Not complex. However, Not4 is important for proper assembly of the proteasome, and the Ccr4-Not complex may have multiple functional modules that participate in protein quality control in different ways. In this work we studied how the functions of the Caf1/Ccr4 and Not4 modules are connected. We concluded that Not4 plays a role in protein quality control independently of the Ccr4 deadenylase, and that it is involved in clearance of aberrant proteins at least in part via the proteasome.
Aspergillus and Penicillium (Eurotiales: Trichocomaceae) in soils of the Brazilian tropical dry forest: diversity in an area 
of environmental preservation.

Soil is a complex biological system that plays a key role for plants and animals, especially in dry forests such as the Caatinga. Fungi from soils, such as Aspergillus and Penicillium, can be used as bioindica- tors for biodiversity conservation. The aim of this study was to isolate and identify species of Aspergillus and Penicillium in soil, from the municipalities of Tupanatinga and Ibimirim, with dry forests, in the Catimbau National Park. Five collections were performed in each area during the drought season of 2012, totaling 25 soil samples per area. Fungi were isolated by suspending soil samples in sterile distilled water and plating on Sabouraud Agar media plus Chloramphenicol and Rose Bengal, and Glycerol Dicloran Agar. Isolates were identified by morphological taxonomy in the Culture Collection Laboratory and confirmed by sequencing of the Internal Transcribed Spacer of rDNA. A total of 42 species were identified, of which 22 belong to the genus Aspergillus and 20 to Penicillium. Penicillium isolates showed uniform distribution from the collecting area in Tupanatinga, and the evenness indices found were 0.92 and 0.88 in Tupanatinga and Ibimirim, respectively. Among isolates of Aspergillus evenness, the value found in Tupanatinga (0.85) was very close to that found in Ibimirim (0.86). High diversity and low dominance of fungi in soil samples was observed. These results con- tributed to the estimation of fungal diversity in dry environments of the Caatinga, where diversity is decreasing in soils that have undergone disturbance.
Ribosomal DNA, tri- and bi-partite pericentromeres in the permanent translocation heterozygote Rhoeo spathacea

High- and low-stringency FISH and base-specific fluorescence were performed on the permanent translocation heterozygote Rhoeo spathacea (2n = 12). Our results indicate that 45S rDNA arrays, rDNA-related sequences and other GC-rich DNA fraction(s) are located within the pericentromeric regions of all twelve chromosomes, usually colocalizing with the chromomycin A3-positive bands. Homogenization of the pericentromeric regions appears to result from the concerted spread of GC-rich sequences, with differential amplification likely. We found new 5S rDNA patterns, which suggest a variability in the breakpoints and in the consequent chromosome reorganizations. It was found that the large 5S rDNA locus residing on each of the 8E and 9E arms consisted of two smaller loci. On each of the two chromosome arms 3b and 4b, in addition to the major subtelomeric 5S rDNA locus, a new minor locus was found interstitially about 40% along the arm length. The arrangement of cytotogenetic landmarks and chromosome arm measurements are discussed with regard to genome repatterning in Rhoeo.
Journal of University Teaching & Learning Practice Journal of University Teaching & Learning Practice

Abstract This paper contributes to the debate on what constitutes good teaching in early 21st Century higher education, through an examination of the experience of five outstanding lecturers from a business school in an Australian university. It is based on a qualitative study that explored their perceptions on what constitutes ‘good teaching’. Resonating with existing research on good teaching practice, the findings suggest that good teachers tend to embrace constructivist principles, and are committed to facilitating learning that is deep, engaged, experientially-based, empowering, reflective, and life-long. The real-life examples of good teaching practice provided by the participants are a valuable resource to higher education teachers, in particular those beginning their careers.
Structural Changes in Poly(trimethylene adipate) and Poly(trimethylene succinate) During Melt Crystallization Studied Using In Situ Infrared Spectroscopy

This paper investigates the structural changes occurring in poly(trimethylene adipate) (PTAd) and poly(trimethylene succinate) (PTSu) during melt crystallization using differential scanning calorimetry (DSC) and in situ Fourier transform infrared (FT-IR) spectroscopy. Cooling thermograms revealed that PTAd had a faster crystallization rate than PTSu. Infrared (IR) bands of the two polyesters were assigned by correlating with the IR bands of polymers containing the trimethylene and the diacid segments. The bands at 1478, 1459, 1393, and 1364 cm−1 in PTAd and 1475, 1459, 1393, and 1361 cm−1 in PTSu were designated to the CH2 of the trimethylene segment. Changes in the IR band absorbance intensities of the CH2 and the C–O–C groups were monitored with time during melt crystallization. Structural changes of the trimethylene and diacid segments of PTAd occurred synchronously, while in PTSu the two segments changed sequentially. Normalized band intensities showed a time lag between the trimethylene and succinic acid segments. The acid segment showed a faster change compared to the trimethylene segment. Fourier transform infrared spectroscopy is shown to be a useful technique to study conformational changes during crystallization in polymers.
Optical coherence tomography angiography and choroidal neovascularization in multifocal choroiditis: A descriptive study

Purpose: To analyze the ability of optical coherence tomography angiography to identify choroidal neovascularization in multifocal choroiditis and to describe active and inactive choroidal neovascularization findings. Methods: Retrospective study of consecutive patients with multifocal choroiditis and choroidal neovascularization examined between January and November 2016. In addition to usual exams, optical coherence tomography angiography (AngioPlex™ CIRRUS™ HD-OCT model 5000; Carl Zeiss Meditec, Inc., Dublin, CA, USA) images were assessed for morphological analysis: choroidal neovascularization size, choroidal neovascularization margin (well or poorly circumscribed), choroidal neovascularization shape (tangled or interlacing), choroidal neovascularization core (feeder vessel) and dark ring around the choroidal neovascularization. Results: A total of 10 eyes were included. Optical coherence tomography angiography identified all choroidal neovascularization. Active choroidal neovascularization had well-circumscribed margins (67%), interlacing shape (83%), and a surrounding dark ring (83%). Inactive choroidal neovascularization had rather poorly circumscribed margins (75%), tangled shape, and “dead tree” appearance (50%) with less frequently a surrounding dark ring (50%). Conclusion: Optical coherence tomography angiography is adapted to confirm the diagnosis of choroidal neovascularization complicating multifocal choroiditis, but it is still insufficient to differentiate active and inactive lesions.
Surface Energy and Wetting in Island Films

The chapter describes the fundamental aspects of the effects of scale on surface phenomena in condensed films. Experimental and theoretical data for the size and temperature dependencies of the surface energy (including the solid phase); wetting of solid surfaces and free thin films by small metal particles are discussed. Several modern methods of contact angle measurement in small-sized systems based on the optical and electron microscopy methods are described.