Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinicopathologic Features of Fatal Non-Anaplastic Follicular Cell-Derived Thyroid Carcinomas.

BACKGROUND The vast majority of thyroid cancers, in particular the non-anaplastic follicular cell-derived thyroid carcinomas (non-ANA FCDC), are considered indolent tumors with very low mortality. Hence, it is crucial to analyze the subgroup of these patients who die of disease (DOD) in order to identify clinicopathologic features predictive of disease-specific mortality. METHODS All non-ANA FCDC operated at a tertiary cancer center between 1985 and 2010 who were DOD were identified and submitted to a meticulous clinicopathologic analysis. RESULTS Out of 3750 non-ANA FCDC, 58 (1.5%) DOD cases were identified. The DOD group was composed of 33 (57%) poorly differentiated carcinomas (PDTC), 14 (24%) tall-cell variant papillary thyroid carcinomas (TCVPTC), four (7%) Hürthle cell carcinomas, three (5%) papillary microcarcinomas, two (3%) classical variant PTC, and two (3%) follicular variant PTC. Twenty-seven (47%) patients presented with distant metastases (DM), 28 (48%) developed DM during follow-up, while the remaining three (5%) had locally advanced non-resectable recurrence. Gross extension beyond the thyroid (GET) was present in 36 (62%) and extensive vascular invasion (VI) in 21 (36%) of cases. All microcarcinomas had PDTC in their clinically apparent cervical lymph nodes at presentation. Encapsulated thyroid carcinomas were responsible for 17% of DOD cases, and all had extensive VI and/or DM at presentation. All patients had at least one of these high-risk features at diagnosis: DM at presentation, PDTC, GET, and/or extensive VI. The majority of patients died from DM (n = 51; 88%), three (5%) from locoregional disease, three (5%) from both, and one (2%) from unknown cause. CONCLUSIONS PDTC and TCVPTC are responsible for the vast majority of deaths in differentiated thyroid carcinomas, while the few fatal classical, follicular variant PTC and microcarcinomas all harbor a PDTC component, DM, or GET. Encapsulated differentiated thyroid carcinoma with focal capsular and/or VI without DM at presentation does not seem to cause death. Lack of DM at presentation, PDTC, GET, and extensive VI identify thyroid carcinomas that are at almost no risk of DOD. The vast majority of patients die of DM rather than locoregional invasion, prompting the need for effective systemic treatment.
Full-Diversity Space-Time Block Codes for Integer-Forcing Linear Receivers

In multiple-input multiple-output (MIMO) fading channels, the design criterion for full-diversity space-time block codes (STBCs) is primarily determined by the decoding method at the receiver. Although constructions of STBCs have predominantly matched the maximum-likelihood (ML) decoder, design criteria and constructions of full-diversity STBCs have also been reported for low-complexity linear receivers. A new receiver architecture called Integer-Forcing (IF) linear receiver has been proposed to MIMO channels by Zhan et al. which showed promising results for the high-rate V-BLAST encoding scheme. In this paper, we address the design of full-diversity STBCs for IF linear receivers. In particular, we are interested in characterizing the structure of STBCs that provide full-diversity with the IF receiver. Along that direction, we derive an upper bound on the probability of decoding error, and show that STBCs that satisfy the restricted non-vanishing singular value (RNVS) property provide full-diversity for the IF receiver. Furthermore, we prove that all known STBCs with the non-vanishing determinant property provide full-diversity with IF receivers, as they guarantee the RNVS property. By using the formulation of RNVS property, we also prove the existence of a full-diversity STBC outside the class of perfect STBCs, thereby adding significant insights compared to the existing works on STBCs with IF decoding. Finally, we present extensive simulation results to demonstrate that linear designs with RNVS property provide full-diversity for IF receiver.
An evaluation of handling and physico-mechanical properties of resin-composite materials

Resin composites are the most commonly used material in restorative dentistry. They have been used initially for aesthetical reasons, but afterwards were modified to be used widely for their good aesthetic and mechanical properties performance. They are classified as visco-elastic materials which are composed of inorganic fillers and organic matrix.The aim of this study was to investigate some handling properties of uncured resin composites such as stickiness, consistency and rheology. Also, to measure the degree of conversion and creep behaviour under static loading of some resin composites.In the pre-cure stage, their handling properties are very essential to achieve a successful dental restoration. Therefore, dental practitioners are very critical in choosing the resin composite restorative material. A texture analyser was used to measure the stickiness and consistency of some commercial resin composites. Also, the rheology of different commercial and model resin composites were investigated using the Bohlin Rheometer in two different temperatures (room and body temperature). Moreover, Fourier transform infrared spectroscopy (FTIR) was used to determine the degree of conversion of several bulk-fill resin composites (DC) at 4 mm depth at different periods during 24 h post-irradiation.Also, the visco-elastic stability of cured resin composites with different resin matrices was investigated under static load at different maturation times (1 h and 24 h).
TRPC1 Deletion Causes Striatal Neuronal Cell Apoptosis and Proteomic Alterations in Mice

Transient receptor potential channel 1 (TRPC1) is widely expressed throughout the nervous system, while its biological role remains unclear. In this study, we showed that TRPC1 deletion caused striatal neuronal loss and significantly increased TUNEL-positive and 8-hydroxy-2′-deoxyguanosine (8-OHdG) staining in the striatum. Proteomic analysis by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) revealed a total of 51 differentially expressed proteins (26 increased and 25 decreased) in the stratum of TRPC1 knockout (TRPC1−/−) mice compared to that of wild type (WT) mice. Bioinformatics analysis showed these dysregulated proteins included: oxidative stress-related proteins, synaptic proteins, endoplasmic reticulum (ER) stress-related proteins and apoptosis-related proteins. STRING analysis showed these differential proteins have a well-established interaction network. Based on the proteomic data, we revealed by Western-blot analysis that TRPC1 deletion caused ER stress as evidenced by the dysregulation of GRP78 and PERK activation-related signaling pathway, and elevated oxidative stress as suggested by increased 8-OHdG staining, increased NADH dehydrogenase (ubiquinone) flavoprotein 2 (NDUV2) and decreased protein deglycase (DJ-1), two oxidative stress-related proteins. In addition, we also demonstrated that TRPC1 deletion led to significantly increased apoptosis in striatum with concurrent decrease in both 14–3–3Z and dynamin-1 (D2 dopamine (DA) receptor binding), two apoptosis-related proteins. Taken together, we concluded that TRPC1 deletion might cause striatal neuronal apoptosis by disturbing multiple biological processes (i.e., ER stress, oxidative stress and apoptosis-related signaling). These data suggest that TRPC1 may be a key player in the regulation of striatal cellular survival and death.
Rotator cuff repair: challenges and solutions

Each year, 250,000 rotator cuff repairs are performed in the United States at a cost of $3 billion. Despite advancements in repair techniques and rehabilitation, 20%-70% of repairs continue to undergo structural failure; however, there is a poor correlation between clinical and structural outcomes, both before and after surgery. "Failure in continuity", or retraction of the repair site without a structural defect, is likely a common phenomenon after rotator cuff repair, and this retraction of the myotendinous unit and interposing scar tissue may be one explanation for the discordance between clinical and structural outcomes. Scaffolds, both synthetic and biologic, have shown promise in both augmentation of repairs and interposition of irreparable tears, but most studies are small retrospective case series without control groups. Future efforts will need to determine the ideal indications for use, methods of application, and comparative effectiveness between the devices. Platelet-rich plasma also has potential to improve rotator cuff healing, but current limitations include the significant variation in preparation methods, biologic makeup, and application methods. Future work may help us understand whether application of platelet-rich plasma and its growth factors should be done at the time of surgery or later during a more advanced stage of healing. Regardless of the device or technique, mechanical and/or biologic augmentation of rotator cuff repairs requires the surgeon to be technically proficient in its use and aware of its associated increased operative time and cost. In order to justify the use of these technologies and their associated incremental cost, we must demonstrate efficacy in improving both clinical and structural outcomes.
Metabolomic Analysis of Cold Acclimation of Arctic Mesorhizobium sp. Strain N33

Arctic Mesorhizobium sp. N33 isolated from nodules of Oxytropis arctobia in Canada’s eastern Arctic has a growth temperature range from 0°C to 30°C and is a well-known cold-adapted rhizobia. The key molecular mechanisms underlying cold adaptation in Arctic rhizobia remains totally unknown. Since the concentration and contents of metabolites are closely related to stress adaptation, we applied GC-MS and NMR to identify and quantify fatty acids and water soluble compounds possibly related to low temperature acclimation in strain N33. Bacterial cells were grown at three different growing temperatures (4°C, 10°C and 21°C). Cells from 21°C were also cold-exposed to 4°C for different times (2, 4, 8, 60 and 240 minutes). We identified that poly-unsaturated linoleic acids 18∶2 (9, 12) & 18∶2 (6, 9) were more abundant in cells growing at 4 or 10°C, than in cells cultivated at 21°C. The mono-unsaturated phospho/neutral fatty acids myristoleic acid 14∶1(11) were the most significantly overexpressed (45-fold) after 1hour of exposure to 4°C. As reported in the literature, these fatty acids play important roles in cold adaptability by supplying cell membrane fluidity, and by providing energy to cells. Analysis of water-soluble compounds revealed that isobutyrate, sarcosine, threonine and valine were more accumulated during exposure to 4°C. These metabolites might play a role in conferring cold acclimation to strain N33 at 4°C, probably by acting as cryoprotectants. Isobutyrate was highly upregulated (19.4-fold) during growth at 4°C, thus suggesting that this compound is a precursor for the cold-regulated fatty acids modification to low temperature adaptation.
Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites

Hemimethylation drives chromatin assembly Cytosine DNA methylation is a heritable and essential epigenetic mark. During DNA replication, cytosines on mother strands remain methylated, but those on daughter strands are initially unmethylated. These hemimethylated sites are rapidly methylated to maintain faithful methylation patterns. Xu and Corces mapped genome-wide strand-specific DNA methylation sites on nascent chromatin, confirming such maintenance in the vast majority of the DNA methylome (see the Perspective by Sharif and Koseki). However, they also identified a small fraction of sites that were stably hemimethylated and showed their inheritance at CTCF (CCCTC-binding factor)/cohesin binding sites. These inherited hemimethylation sites were required for CTCF and cohesin to establish proper chromatin interactions. Science, this issue p. 1166; see also p. 1102 Stably inherited hemimethylation surrounding CTCF motifs is required for CTCF-mediated chromatin interactions. The faithful inheritance of the epigenome is critical for cells to maintain gene expression programs and cellular identity across cell divisions. We mapped strand-specific DNA methylation after replication forks and show maintenance of the vast majority of the DNA methylome within 20 minutes of replication and inheritance of some hemimethylated CpG dinucleotides (hemiCpGs). Mapping the nascent DNA methylome targeted by each of the three DNA methyltransferases (DNMTs) reveals interactions between DNMTs and substrate daughter cytosines en route to maintenance methylation or hemimethylation. Finally, we show the inheritance of hemiCpGs at short regions flanking CCCTC-binding factor (CTCF)/cohesin binding sites in pluripotent cells. Elimination of hemimethylation causes reduced frequency of chromatin interactions emanating from these sites, suggesting a role for hemimethylation as a stable epigenetic mark regulating CTCF-mediated chromatin interactions.
Modelling CdTe thin film growth over realistic time scales

Cadmium Telluride (CdTe) is an excellent material for low-cost, high efficiency thin-film solar cells and holds the record for watts/cost performance. The laboratory record efficiency of CdTe solar cells lags significantly behind the theoretical maximum for the material. This discrepancy is often attributed to defects such as grain boundaries and dislocations. Thus it is important to do research on how these defects are formed during the growth process. Atomistic simulations, such as Molecular Dynamics (MD) and on-the-fly Kinetic Monte Carlo (OTF-KMC), are widely used in partnership with experiments in addressing problems in materials science. In this work we use computer simulation to predict the growth of the sputter deposited CdTe thin film. At the first stage, MD studies of small cluster energetic impacts were carried out by repeatedly depositing CdxTey (x, y = 0, 1) clusters onto different CdTe surfaces with different energies at random positions. The impacts were simulated on Cd- and Te-terminated (100) surfaces and Cd- and Te-terminated (111) surfaces with typical industrial energies varies from 1 to 40 eV at a temperature of 350 K. More than 1,000 simulations have been preformed for each of these cases so as to sample the possible deposition positions and to collect sufficient statistics. The behaviour of deposited clusters under different conditions are studies. To simulate the process of thin film growth is the next stage in this work. We use different techniques to simulate the growth process on different surfaces. OTF-KMC simulations are performed to simulate the thin film growth process on the (111) CdTe surfaces. Starting with several ad-atoms deposited on the surfaces, in each step, the OTF-KMC method searches for all possible atomic movements (transitions) and randomly selects a transition or deposition to execute based on their corresponding rates. The thin film grows with more and more clusters to be deposited onto the surface with numerous ad-atom diffusions. The growth process on the dimerised Te-terminated (100) surface is very interesting. Knowledge of how the Te dimers on the surface split during the growth is gained in the simulations. MD is used to simulate the growth process with an accelerated deposition rate. Several simulations with different deposition energies are performed to see the differences of dissociation of the surface Te dimers. Post-annealing at different temperatures are applied after the growth simulations to find the optimal annealing temperature.
Written in bone: young bone makes young blood

Ageing of bone marrow haematopoietic stem cells has been mostly associated with cell‐intrinsic mechanisms. New findings published in The EMBO Journal now show that reduced levels of the secreted matrix protein osteopontin in old bone marrow stroma cause ageing‐associated features in HSCs. In line, old HSCs are functionally rejuvenated by interaction with protease‐cleaved osteopontin fragment, and perform like young blood stem cells in vivo.
Disruption of the transient receptor potential vanilloid 1 can affect survival, bacterial clearance, and cytokine gene expression during murine sepsis.

BACKGROUND Previous studies suggest that the transient receptor potential vanilloid 1 (TRPV1) channel has a role in sepsis, but it is unclear whether its effect on survival and immune response is beneficial or harmful. METHODS We studied the effects of genetic (Trpv1-knockout vs. wild-type [WT] mice) and pharmacologic disruption of TRPV1 with resiniferatoxin (an agonist) or capsazepine (an antagonist) on mortality, bacterial clearance, and cytokine expression during lipopolysaccharide or cecal ligation and puncture-induced sepsis. RESULTS After cecal ligation and puncture, genetic disruption of TRPV1 in Trpv1-knockout versus WT mice was associated with increased mortality risk (hazard ratio, 2.17; 95% CI, 1.23-3.81; P = 0.01). Furthermore, pharmacologic disruption of TRPV1 with intrathecal resiniferatoxin, compared with vehicle, increased mortality risk (hazard ratio, 1.80; 95% CI, 1.05-3.2; P = 0.03) in WT, but not in Trpv1-knockout, mice. After lipopolysaccharide, neither genetic (Trpv1 knockout) nor pharmacologic disruption of TRPV1 with resiniferatoxin had significant effect on survival compared with respective controls. In contrast, after lipopolysaccharide, pharmacologic disruption of TRPV1 with capsazepine, compared with vehicle, increased mortality risk (hazard ratio, 1.92; 95% CI, 1.02-3.61; P = 0.04) in WT animals. Furthermore, after cecal ligation and puncture, increased mortality in resiniferatoxin-treated WT animals was associated with higher blood bacterial count (P = 0.0004) and higher nitrate/nitrite concentrations and down-regulation of tumor necrosis factor α expression (P = 0.004) compared with controls. CONCLUSIONS Genetic or pharmacologic disruption of TRPV1 can affect mortality, blood bacteria clearance, and cytokine response in sepsis in patterns that may vary according to the sepsis-inducing event and the method of TRPV1 disruption.
The efficacy of a HUBER exercise system mediated sensorimotor training protocol on proprioceptive system, lumbar movement control and quality of life in patients with chronic non-specific low back pain.

BACKGROUND There is a relation between deficits of the proprioceptive system and movement control dysfunction in patients with chronic low back pain (LBP) but, the exact mechanism of this relation is unknown. Exercise therapy has been recognized as an effective method for low back pain treatment. In spite of this, it is not clear which of the various exercise therapy programs lead to better results. OBJECTIVE Therefore, the present analyze the efficacy of a HUBER study aims to exercise system mediated sensorimotor training protocol on proprioceptive system, lumbar movement control (LMC) and quality of life (QOL) in patients with chronic non-specific LBP. DESIGN Quasi-experimental study. METHODS 53 patients with chronic non-specific LBP (mean age 37.55 ± 6.67 years,and Body Mass Index (BMI) 22.4 ± 3.33) were selected by using Roland-Morris Disability Questionnaire (RMQ) and were assigned into two experimental (N= 27) and control groups (N= 26) The experimental group underwent a five-week (10 sessions) Sensorimotor training by using the Human Body Equalizer (HUBER) spine force under the supervision of an investigator. The movement control battery tests, the HUBER machine testing option, goniometer and visual analogue scale used for movement control, neuromuscular coordination, proprioception and LBP assessment respectively. The assessments were completed in pre-test and after five weeks. The paired and sample T tests were used for data analysis in SPSS program version 18 (Significance level were set at a P value < 0.05). RESULTS The HUBER system mediated sensorimotor training demonstrated significant improvement in the proprioceptive system, LMC and QOL (P= 0.001). Also There was a significant reduction in the pain scores of subjects with chronic non-specific LBP in the sensorimotor group (P= 0.001). LIMITATIONS In this study, only the short term effects of the sensorimotor training were examined. CONCLUSIONS The results suggest that a sensorimotor training program causes significant improvement in patients with chronic non-specific LBP. Future research should be carried out with a larger sample size to examine the long term effects of the sensorimotor training program on treatment of patients with chronic non-specific LBP. Considering the efficacy of the sensorimotor training, it is recommended that this intervention should be applied to treatment of patients with chronic non-specific LBP in the future.
Defending against Adversarial Images using Basis Functions Transformations

We study the effectiveness of various approaches that defend against adversarial attacks on deep networks via manipulations based on basis function representations of images. Specifically, we experiment with low-pass filtering, PCA, JPEG compression, low resolution wavelet approximation, and soft-thresholding. We evaluate these defense techniques using three types of popular attacks in black, gray and white-box settings. Our results show JPEG compression tends to outperform the other tested defenses in most of the settings considered, in addition to soft-thresholding, which performs well in specific cases, and yields a more mild decrease in accuracy on benign examples. In addition, we also mathematically derive a novel white-box attack in which the adversarial perturbation is composed only of terms corresponding a to pre-determined subset of the basis functions, of which a "low frequency attack" is a special case.