Miracle-dz/UniFAR-FTUs huggingface dataset:
Adipose-Induced Retroperitoneal Soft Tissue Sarcoma Tumorigenesis: A Potential Crosstalk between Sarcoma and Fat Cells

Previous data demonstrated that high retroperitoneal visceral fat content increases retroperitoneal soft-tissue sarcoma (RSTS) local recurrence and patients' mortality. Most RSTS tumors initiate and recur within visceral fat. The objective of the current study was to evaluate potential paracrine effects of visceral fat on RSTS. A xenograft model was used to evaluate in vivo effects of human visceral fat on STS growth. Tissue explants were prepared from visceral fat, and their conditioned medium (CM) was utilized for various in vitro experiments designed to evaluate growth, survival, migration, and invasion of STS and endothelial cells. Visceral fat–secreted protumorigenic factors were identified by mass spectrometry. The in vivo experiments demonstrated a significant increase in STS tumor growth rate when SK-LMS-1 leiomyosarcoma cells were colocalized with human visceral fat compared with subcutaneous injection of cancer cells only. The in vitro model demonstrated that visceral fat CM increased STS cellular growth and reduced doxorubicin-induced apoptosis. Visceral fat also enhanced STS cellular migration and invasion. In addition, visceral fat CM significantly increased endothelial cell tube formation, suggesting its role as a proangiogenic factor in the STS tumor microenvironment (TME). Using a robust proteomic approach, liquid chromatography and tandem mass spectrometry resolved various molecules within the visceral fat CM, of which a subset was associated with protumorigenic biologic processes. These results suggest that visceral fat directly interacts with STS cells by secreting specific adipokines into the TME, thus augmenting STS tumor cell proliferation and invasiveness. Fat-induced STS molecular deregulations should be studied to identify new potential prognostic and therapeutic targets. Implications: Visceral fat induces protumorigenic effects, in STS, through various secreted factors that should be investigated to improve our understanding of adipose–cancer cell interactions. Mol Cancer Res; 14(12); 1254–65. ©2016 AACR.
Resistance to anticancer immunity in cancer patients: potential strategies to reverse resistance

In the 1990s, the application of immunotherapy approaches to target cancer cells resulted in significant clinical responses in patients with advanced malignancies who were refractory to conventional therapies. While early immunotherapeutics were focused on T cell-mediated cytotoxic activity, subsequent efforts were centered on targeted antibody-mediated anticancer therapy. The initial success with antibody therapy encouraged further studies and, consequently, there are now more than 25 FDA-approved antibodies directed against a range of targets. Although both T cell and antibody therapies continue to result in significant clinical responses with minimal toxicity, a significant subset of patients does not respond to immunotherapy and another subset develops resistance following an initial response. This review is focused on describing examples showing that cancer resistance to immunotherapies indeed occurs. In addition, it reviews the mechanisms being used to overcome the resistance to immunotherapies by targeting the tumor cell directly and/or the tumor microenvironment.
Effects of Short-Term Free-Weight and Semiblock Periodization Resistance Training on Metabolic Syndrome

Abstract South, MA, Layne, AS, Stuart, CA, Triplett, NT, Ramsey, MW, Howell, ME, Sands, WA, Mizuguchi, S, Hornsby, WG, Kavanaugh, AA, and Stone, MH. Effects of short-term free-weight and semiblock periodization resistance training on metabolic syndrome. J Strength Cond Res 30(10): 2682–2696, 2016—The effects of short-term resistance training on performance and health variables associated with prolonged sedentary lifestyle and metabolic syndrome (MS) were investigated. Resistance training may alter a number of health-related, physiological, and performance variables. As a result, resistance training can be used as a valuable tool in ameliorating the effects of a sedentary lifestyle including those associated with MS. Nineteen previously sedentary subjects (10 with MS and 9 with nonmetabolic syndrome [NMS]) underwent 8 weeks of supervised resistance training. Maximum strength was measured using an isometric midthigh pull and resulting force-time curve. Vertical jump height (JH) and power were measured using a force plate. The muscle cross-sectional area (CSA) and type were examined using muscle biopsy and standard analysis techniques. Aerobic power was measured on a cycle ergometer using a ParvoMedics 2400 Metabolic system. Endurance was measured as time to exhaustion on a cycle ergometer. After training, maximum isometric strength, JH, jump power, and V[Combining Dot Above]O2peak increased by approximately 10% (or more) in both the metabolic and NMS groups (both male and female subjects). Over 8 weeks of training, body mass did not change statistically, but percent body fat decreased in subjects with the MS and in women, and lean body mass increased in all groups (p ⩽ 0.05). Few alterations were noted in the fiber type. Men had larger CSAs compared those of with women, and there was a fiber-specific trend toward hypertrophy over time. In summary, 8 weeks of semiblock free-weight resistance training improved several performance variables and some cardiovascular factors associated with MS.
Early-Life Epilepsies and the Emerging Role of Genetic Testing

Importance Early-life epilepsies are often a consequence of numerous neurodevelopmental disorders, most of which are proving to have genetic origins. The role of genetic testing in the initial evaluation of these epilepsies is not established. Objective To provide a contemporary account of the patterns of use and diagnostic yield of genetic testing for early-life epilepsies. Design, Setting, and Participants In this prospective cohort, children with newly diagnosed epilepsy with an onset at less than 3 years of age were recruited from March 1, 2012, to April 30, 2015, from 17 US pediatric hospitals and followed up for 1 year. Of 795 families approached, 775 agreed to participate. Clinical diagnosis of the etiology of epilepsy were characterized based on information available before genetic testing was performed. Added contributions of cytogenetic and gene sequencing investigations were determined. Exposures Genetic diagnostic testing. Main Outcomes and Measures Laboratory-confirmed pathogenic variant. Results Of the 775 patients in the study (367 girls and 408 boys; median age of onset, 7.5 months [interquartile range, 4.2-16.5 months]), 95 (12.3%) had acquired brain injuries. Of the remaining 680 patients, 327 (48.1%) underwent various forms of genetic testing, which identified pathogenic variants in 132 of 327 children (40.4%; 95% CI, 37%-44%): 26 of 59 (44.1%) with karyotyping, 32 of 188 (17.0%) with microarrays, 31 of 114 (27.2%) with epilepsy panels, 11 of 33 (33.3%) with whole exomes, 4 of 20 (20.0%) with mitochondrial panels, and 28 of 94 (29.8%) with other tests. Forty-four variants were identified before initial epilepsy presentation. Apart from dysmorphic syndromes, pathogenic yields were highest for children with tuberous sclerosis complex (9 of 11 [81.8%]), metabolic diseases (11 of 14 [78.6%]), and brain malformations (20 of 61 [32.8%]). A total of 180 of 446 children (40.4%), whose etiology would have remained unknown without genetic testing, underwent some testing. Pathogenic variants were identified in 48 of 180 children (26.7%; 95% CI, 18%-34%). Diagnostic yields were greater than 15% regardless of delay, spasms, and young age. Yields were greater for epilepsy panels (28 of 96 [29.2%]; P < .001) and whole exomes (5 of 18 [27.8%]; P = .02) than for chromosomal microarray (8 of 101 [7.9%]). Conclusions and Relevance Genetic investigations, particularly broad sequencing methods, have high diagnostic yields in newly diagnosed early-life epilepsies regardless of key clinical features. Thorough genetic investigation emphasizing sequencing tests should be incorporated into the initial evaluation of newly presenting early-life epilepsies and not just reserved for those with severe presentations and poor outcomes.
A review of 111 anaesthetic patients undergoing cytoreductive surgery and hyperthermic intraperitoneal chemotherapy.

INTRODUCTION Cytoreductive surgery (CRS) along with hyperthermic intraperitoneal chemotherapy (HIPEC) is the treatment of choice for selected patients with peritoneal carcinomatosis, a previously lethal condition with dismal survival rates. METHODS We reviewed CRS and HIPEC procedures performed at our centre from January 1997 to December 2012, focusing on perioperative events and anaesthetic implications. RESULTS In total, 111 patients underwent 113 procedures. Mean age of the patients was 51.7 (range 14-74) years and 84.1% were women. Mean duration of surgery was 9 hours 10 minutes ± 2 hours 56 minutes. Most tumours were ovarian or colorectal in origin, and the mean peritoneal cancer index (PCI) score was 14.3 ± 8.9. Mean estimated blood loss was 1,481 ± 1,064 mL. Mean total intravenous fluids and blood products administered was 8,498 ± 3,941 mL. Postoperatively, 79.5% of the patients needed intensive care, as 75.2% of the 113 procedures required interval extubation. Patients with lower PCI scores were more likely to be extubated immediately after surgery (p < 0.05). 80.0% of patients had coagulopathy postoperatively, and this was associated with longer HIPEC duration (p < 0.05). Median lengths of intensive care unit and hospital stays were two days and 14 days, respectively. Longer duration of surgery significantly correlated with longer hospitalisation. Prolonged hospitalisation was due to nosocomial pneumonia, pleural effusions, respiratory failure, sepsis, surgical complications (such as anastomotic or wound dehiscence), and intra-abdominal infections. CONCLUSION The CRS and HIPEC technique is a major surgery with significant morbidity, as highlighted by the perioperative concerns observed in our study.
Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic

In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid’s gladius—the chitinous spiniform structure supporting the muscles and organs—were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid’s trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from lower to higher trophic levels may be underestimated and important for understanding how a changing ocean impacts food webs in the eastern Atlantic.
The Moral Standing of Animals: Towards a Psychology of Speciesism

We introduce and investigate the philosophical concept of ‘speciesism’ — the assignment of different moral worth based on species membership — as a psychological construct. In five studies, using both general population samples online and student samples, we show that speciesism is a measurable, stable construct with high interpersonal differences, that goes along with a cluster of other forms of prejudice, and is able to predict real-world decision-making and behavior. In Study 1 we present the development and empirical validation of a theoretically driven Speciesism Scale, which captures individual differences in speciesist attitudes. In Study 2, we show high test-retest reliability of the scale over a period of four weeks, suggesting that speciesism is stable over time. In Study 3, we present positive correlations between speciesism and prejudicial attitudes such as racism, sexism, homophobia, along with ideological constructs associated with prejudice such as social dominance orientation, system justification, and right-wing authoritarianism. These results suggest that similar mechanisms might underlie both speciesism and other well-researched forms of prejudice. Finally, in Studies 4 and 5, we demonstrate that speciesism is able to predict prosociality towards animals (both in the context of charitable donations and time investment) and behavioral food choices above and beyond existing related constructs. Importantly, our studies show that people morally value individuals of certain species less than others even when beliefs about intelligence and sentience are accounted for. We conclude by discussing the implications of a psychological study of speciesism for the psychology of human-animal relationships.
Effects of biomass-burning-derived aerosols on precipitation and clouds in the Amazon Basin: a satellite-based empirical study

[1] Biomass burning in the Amazon provides strong input of aerosols into the atmosphere, with potential effects on precipitation, cloud properties, and radiative balance. However, few studies to date have systematically examined these effects at the scale of the Amazon Basin, over an entire burning season, using available data sets. We empirically study the relationships of aerosol optical depth (ta) versus rainfall and cloud properties measured from satellites over the entire Brazilian Amazon during the dry, biomass burning seasons (August–October) of 2000 and 2003. Elevated ta was associated with increased rainfall in both 2000 and 2003. With enhanced ta, cloud cover increased significantly, and cloud top temperature/pressure decreased, suggesting higher cloud tops. The cloud droplet effective radius (Re) exhibited minimal growth with cloud height under background levels of ta, while distinct increases in Re at cloud top temperatures below � 10C, indicative of ice formation, were observed with aerosol loading. Although empirical correlations do not unequivocally establish the causal link from aerosols, these results are consistent with previous observational and modeling studies that pointed to dynamical effects from aerosols that invigorate convection, leading to higher clouds, enhanced cloud cover, and stronger rainfall. We speculate that changes in precipitation and cloud properties associated with aerosol loading observed in this study could have important radiative and hydrological effects on the Amazonian climate system. The accelerated forest burning for agricultural land clearing and the resulting enhancements in aerosols and rainfall may even partially account for the observed positive trend in Amazonian precipitation over the past several decades. Citation: Lin, J. C. , T. Matsui, R. A. Pielke Sr., and C. Kummerow (2006), Effects of biomass-burning-derived aerosols on precipitation and clouds in the Amazon Basin: a satellite-based empirical study, J. Geophys. Res., 111, D19204,
Is Our Self Nothing but Reward? Neuronal Overlap and Distinction between Reward and Personal Relevance and Its Relation to Human Personality

Background The attribution of personal relevance, i.e. relating internal and external stimuli to establish a sense of belonging, is a common phenomenon in daily life. Although previous research demonstrated a relationship between reward and personal relevance, their exact neuronal relationship including the impact of personality traits remains unclear. Methodology/Principal Findings Using functional magnetic resonance imaging, we applied an experimental paradigm that allowed us to explore the neural response evoked by reward and the attribution of personal relevance separately. We observed different brain regions previously reported to be active during reward and personal relevance, including the bilateral caudate nucleus and the pregenual anterior cingulate cortex (PACC). Additional analysis revealed activations in the right and left insula specific for the attribution of personal relevance. Furthermore, our results demonstrate a negative correlation between signal changes in both the PACC and the left anterior insula during the attribution of low personal relevance and the personality dimension novelty seeking. Conclusion/Significance While a set of subcortical and cortical regions including the PACC is commonly involved in reward and personal relevance, other regions like the bilateral anterior insula were recruited specifically during personal relevance. Based on our correlation between novelty seeking and signal changes in both regions during personal relevance, we assume that the neuronal response to personally relevant stimuli is dependent on the personality trait novelty seeking.
Vhl deletion in osteoblasts boosts cellular glycolysis and improves global glucose metabolism

The skeleton has emerged as an important regulator of systemic glucose homeostasis, with osteocalcin and insulin representing prime mediators of the interplay between bone and energy metabolism. However, genetic evidence indicates that osteoblasts can influence global energy metabolism through additional, as yet unknown, mechanisms. Here, we report that constitutive or postnatally induced deletion of the hypoxia signaling pathway component von Hippel–Lindau (VHL) in skeletal osteolineage cells of mice led to high bone mass as well as hypoglycemia and increased glucose tolerance, not accounted for by osteocalcin or insulin. In vitro and in vivo data indicated that Vhl-deficient osteoblasts displayed massively increased glucose uptake and glycolysis associated with upregulated HIF-target gene expression, resembling the Warburg effect that typifies cancer cells. Overall, the glucose consumption by the skeleton was increased in the mutant mice, as revealed by 18F-FDG radioactive tracer experiments. Moreover, the glycemia levels correlated inversely with the level of skeletal glucose uptake, and pharmacological treatment with the glycolysis inhibitor dichloroacetate (DCA), which restored glucose metabolism in Vhl-deficient osteogenic cells in vitro, prevented the development of the systemic metabolic phenotype in the mutant mice. Altogether, these findings reveal a novel link between cellular glucose metabolism in osteoblasts and whole-body glucose homeostasis, controlled by local hypoxia signaling in the skeleton.
Edlib: a C/C++ library for fast, exact sequence alignment using edit distance

We present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we expect it to be a cornerstone for many future bioinformatics tools. Source code, installation instructions and test data are freely available for download at https://github.com/Martinsos/edlib, implemented in C/C++ and supported on Linux, MS Windows, and Mac OS. Contact: mile.sikic@fer.hr
The Spectrum of Biopsy-Proven Glomerular Disease in China: A Systematic Review

Background: Chronic kidney disease has become a leading public health concern in China, as it is associated with increased morbidity, mortality, and costs. However, the overall situation regarding common glomerular diseases in China remains unclear. Hence, the aim of this study was to assess the national profile of the common types of glomerulonephritis in China. Methods: We searched Medline, Embase, Cochrane Library, CNKI, SinoMed, VIP, and Wanfang databases for English and Chinese language articles from inception to September 2017. We also collected potentially relevant studies and reviews using a manual search. The following words in combinations are as keywords: “renal biopsy”, “kidney pathological diagnosis”, and “spectrum of pathological types”. Results: We identified 23 studies involving 176,355 patients from 15 provinces/cities in China. The detection rates of primary glomerulonephritis (PGN) and secondary glomerulonephritis (SGN) were 0.740 and 0.221, respectively. Over the past 30 years, the top five types of PGN were immunoglobulin A nephropathy (IgAN; 24.3%), mesangial proliferative glomerulonephritis (MsPGN; 10.5%), membranous nephropathy (MN; 12.6%), minimal change disease (MCD; 9.8%), and focal segmental glomerulosclerosis (FSGS; 4.6%), and the top four types of SGN were lupus nephritis (LN; 8.6%), Henoch-Schönlein purpura glomerulonephritis (4.1%), hepatitis B virus-associated glomerulonephritis (HBV-GN; 2.6%), and diabetic nephropathy (DN; 1.6%). The proportion of MN, MCD, HBV-GN, and DN tended to increase, while those of IgAN, MsPGN, FSGS, and LN tended to drop. Conclusions: Although the incidence of SGN is increasing gradually, PGN is still the leading form of kidney disease in patients undergoing renal biopsies in China. IgAN and LN are the most common types of PGN and SGN, respectively. Differences between regions are related to various factors such as nationality, environment, and diet. Furthermore, unified standards and norms for evaluating renal biopsies are urgently needed.
The effect of hemodialysis on intraocular pressure.

BACKGROUND The effect of hemodialysis (HD) on intraocular pressure (IOP) has been investigated before, but there is a lack of consensus. Clinicians dealing with renal failure patients are interested in the potential negative effects of HD on IOP and the course of glaucoma. OBJECTIVES The aim of this study was to investigate the effects of HD on IOP in patients with end-stage renal disease. MATERIAL AND METHODS This prospective study included 106 patients who were receiving outpatient hemodialysis. Patient history of systemic and ophthalmologic conditions was recorded. Serum osmolality (mOsm), blood urea nitrogen (BUN), blood glucose (BG), bicarbonate (BC), and hematocrit (Hct) levels at the start of HD (pre-HD), at the end of HD (end-HD), and 30 min after HD (post-HD) were measured. Systolic and diastolic blood pressures (SBP and DBP) and IOP were measured at pre-HD, 1-hour intervals during HD, end-HD, and post-HD. RESULTS A significant decrease in mOsm and BUN and a significant increase in BG, BC, and Hct levels were observed at end-HD (p < 0.05). Mean IOP was 16.71 ±2.51 mm Hg at pre-HD, 15.52 ±3.18 mm Hg at endHD, and 15.23 ±2.73 mm Hg at post-HD (p = 0.001; F = 4.439). Post-HD SBP and DBP were significantly lower than at pre-HD (p < 0.001). There was a positive correlation between the change in IOP and the change in mOsm and the change in BUN at end-HD (r = 0.315, p = 0.004; and r = 0.279, p = 0.012, respectively). CONCLUSIONS IOP decreased significantly during HD in this study. Additional research on the effects of the change in blood parameters and ocular perfusion pressure on IOP and optic nerve perfusion during HD is recommended.