Miracle-dz/UniFAR-FTUs huggingface dataset:
Mesopelagic microbial community dynamics in response to increasing oil and Corexit 9500 concentrations

Marine microbial communities play an important role in biodegradation of subsurface plumes of oil that form after oil is accidentally released from a seafloor wellhead. The response of these mesopelagic microbial communities to the application of chemical dispersants following oil spills remains a debated topic. While there is evidence that contrasting results in some previous work may be due to differences in dosage between studies, the impacts of these differences on mesopelagic microbial community composition remains unconstrained. To answer this open question, we exposed a mesopelagic microbial community from the Gulf of Mexico to oil alone, three concentrations of oil dispersed with Corexit 9500, and three concentrations of Corexit 9500 alone over long periods of time. We analyzed changes in hydrocarbon chemistry, cell abundance, and microbial community composition at zero, three and six weeks. The lowest concentration of dispersed oil yielded hydrocarbon concentrations lower than oil alone and microbial community composition more similar to control seawater than any other treatments with oil or dispersant. Higher concentrations of dispersed oil resulted in higher concentrations of microbe-oil microaggregates and similar microbial composition to the oil alone treatment. The genus Colwellia was more abundant when exposed to multiple concentrations of dispersed oil, but not when exposed to dispersant alone. Conversely, the most abundant Marinobacter amplicon sequence variant (ASV) was not influenced by dispersant when oil was present and showed an inverse relationship to the summed abundance of Alcanivorax ASVs. As a whole, the data presented here show that the concentration of oil strongly impacts microbial community response, more so than the presence of dispersant, confirming the importance of the concentrations of both oil and dispersant in considering the design and interpretation of results for oil spill simulation experiments.
ATFS-1 plays no repressive role in the regulation of epidermal immune response

Fungal infection triggers the induction of antimicrobial peptide (AMP) genes in the epidermis (Pujol et al, 2008). We previously showed that this effect is suppressed by the mitochondrial unfolded protein response (UPRmt), which can be activated by knockdown of select genes including the mitochondrial metalloprotease spg-7 (Zugasti et al, 2016). Here, we confirm that RNAi against spg-7 triggers the UPRmt and blocks AMP induction during infection, whereas infection itself does not trigger the UPRmt. ATFS-1 is a key factor in the UPRmt, mediating much of the associated transcriptional response. We find that, surprisingly, ATFS-1 is not required for the suppression of AMP induction provoked by spg-7(RNAi). These data show that the mitochondrial dysfunction that blocks the immune response upon infection or wounding is independent of ATFS-1.
More on the invisibility of chronic kidney disease… and counting

ABSTRACT Lack of awareness of a diagnosis of chronic kidney disease (CKD) in patients and physicians is a major contributor to fueling the CKD pandemic by also making it invisible to researchers and health authorities. This is an urgent matter to tackle if dire predictions of future CKD burden are to be addressed. CKD is set to become the fifth-leading global cause of death by 2040 and the second-leading cause of death before the end of the century in some countries with long life expectancy. Coronavirus disease 2019 (COVID-19) illustrated this invisibility: only after the summer of 2020 did it become clear that CKD was a major driver of COVID-19 mortality, both in terms of prevalence as a risk factor and of the risk conferred for lethal COVID-19. However, by that time the damage was done: news outlets and scientific publications continued to list diabetes and hypertension, but not CKD, as major risk factors for severe COVID-19. In a shocking recent example from Sweden, CKD was found to be diagnosed in just 23% of 57 880 persons who fulfilled diagnostic criteria for CKD. In the very same large cohort, diabetes or cancer were diagnosed in 29% of persons, hypertension in 82%, cardiovascular disease in 39% and heart failure in 28%. Thus, from the point of view of physicians, patients and health authorities, CKD was the least common comorbidity in persons with CKD, ranking sixth, after other better-known conditions. One of the consequences of this lack of awareness was that nephrotoxic medications were more commonly prescribed in patients with CKD who did not have a diagnosis of CKD. Low awareness of CKD may also fuel concepts such as the high prevalence of hypertensive nephropathy when CKD is diagnosed after the better-known condition of hypertension.
Immunoglobin A Deficiency and Squamous Cell Carcinoma With a Rare Presentation as Anal Cancer

Selective immunoglobin A deficiency (IgAD) is the most common immunodeficiency disorder in the western world. Cancer is the most common cause of death in these individuals. Various cases have been reported of squamous cell carcinoma (SCC) in IgAD at sites like skin, oral cavity, and lung. Here we present a rare case of SCC occurring as anal cancer. No other reports to our knowledge describe this rare presentation. A 54-year-old Caucasian woman with asymptomatic partial IgAD presented with a palpable anal mass. Further evaluation showed stage IIIa SCC anal cancer (T1N1M0). Additional workup showed positive human papilloma virus (HPV) serology and positive HPV immunohistochemistry studies. The patient achieved complete response with chemoradiation with her most recent imaging and anorectal exam showing no evidence of cancer recurrence at 3 years follow-up. This case highlights the association between IgAD and malignancy. Although IgAD is the most common primary antibody deficiency, this patient’s case presents a rare instance of anal SCC in an IgA-deficient individual. Studies show an association between HPV infection and SCC, but few include IgA-deficient individuals. Patients with IgAD and other immunodeficiencies are at higher risk for HPV infection and therefore may be at a higher risk of SCC. With widespread use of the HPV vaccine, the medical community should be aware of its importance in cancer prevention for these patients. Further studies are needed to evaluate relationships between IgAD, HPV infections, SCC cancer, and the role that the HPV vaccine has in cancer prophylaxis.
The effect of Preoperative threshold inspiratory muscle training in adults undergoing cardiac surgery on postoperative hospital stay: a systematic review

ABSTRACT Background Systematic reviews have reported benefits of preoperative inspiratory muscle training in adults undergoing cardiac surgery, however there have been inconsistencies with the devices used. Threshold devices generate a constant inspiratory load independent of respiratory rate. Objective To assess the effect of preoperative inspiratory muscle training using threshold devices in adults undergoing cardiac surgery. Methods A literature search was conducted across five electronic databases. Seven randomized controlled trials met the inclusion criteria and were critically appraised. The primary outcome was length of hospital stay. Secondary outcomes included postoperative pulmonary complications, quality of life and mortality. Results Seven eligible randomized controlled trials were identified with a total of 642 participants. One study was a post hoc analysis of one of the included studies. Three out of five studies reported a decrease in length of postoperative hospital stay (p < 0.05). A significant reduction in postoperative pulmonary complications was reported by three studies (p < 0.05). There were concerns with bias across all papers. Conclusions Preoperative threshold inspiratory muscle training has potential to reduce postoperative length of hospital stay and pulmonary complications after cardiac surgery. The evidence on quality of life and mortality is inconclusive. The overall evidence for these conclusions may be influenced by bias.
Paving the Way for a Green Transition in the Design of Sensors and Biosensors for the Detection of Volatile Organic Compounds (VOCs)

The efficient and selective detection of volatile organic compounds (VOCs) provides key information for various purposes ranging from the toxicological analysis of indoor/outdoor environments to the diagnosis of diseases or to the investigation of biological processes. In the last decade, different sensors and biosensors providing reliable, rapid, and economic responses in the detection of VOCs have been successfully conceived and applied in numerous practical cases; however, the global necessity of a sustainable development, has driven the design of devices for the detection of VOCs to greener methods. In this review, the most recent and innovative VOC sensors and biosensors with sustainable features are presented. The sensors are grouped into three of the main industrial sectors of daily life, including environmental analysis, highly important for toxicity issues, food packaging tools, especially aimed at avoiding the spoilage of meat and fish, and the diagnosis of diseases, crucial for the early detection of relevant pathological conditions such as cancer and diabetes. The research outcomes presented in the review underly the necessity of preparing sensors with higher efficiency, lower detection limits, improved selectivity, and enhanced sustainable characteristics to fully address the sustainable manufacturing of VOC sensors and biosensors.
The experience of use of percutaneous transhepatic biliary drainages for early biliary complications after liver transplantation

This study aimed to describe our experience and discuss the results, controversies, and the use of percutaneous transhepatic biliary drainage (PTBD) in patients with biliary complications after liver transplantation (LT). Between November 2009 and August 2020, 76 consecutive patients who underwent 77 LTs (44 deceased donor LTs and 33 living donor LTs [LDLT]) were enrolled retrospectively. Endoscopic therapy as initial approach and PTBD as rescue therapy were used for patients with biliary complications. There were 31 patients (31/76, 40.8%) with biliary complications, and two of them died (2/31, 6.5%). Clinical success rate of endoscopic therapy alone was 71.0% (22/31). The remaining nine patients received salvage PTBD and their clinical results were observed according to whether their intrahepatic bile ducts (IHBDs) was dilated (group A, n = 5) or not (group B, n = 4). In group A, the technical and long‐term clinical success rates of PTBD were 100% and 20%, respectively. These five patients received PTBD ranging from 75 to 732 days after their LTs, and no procedure‐related complications were encountered. In group B, the technical and long‐term clinical success rates of PTBD were 50% and 25%, respectively. Three group B patients (75%) underwent PTBD within 30 days after LDLT and had lethal complications. One patient had graft laceration and survived after receiving timely re‐transplantation. The other two patients died of sepsis due to PTBD‐related bilioportal fistula or multiple liver abscesses. Our experience showed salvage PTBD played a limited role in biliary complications without dilated IHBDs within 1 month after LT.
Cerebral Autoregulation Correlation With Outcomes and Spreading Depolarization in Aneurysmal Subarachnoid Hemorrhage

Background: Delayed cerebral ischemia remains one of the principal therapeutic targets after aneurysmal subarachnoid hemorrhage. While large vessel vasospasm may contribute to ischemia, increasing evidence suggests that physiological impairment through disrupted impaired cerebral autoregulation (CA) and spreading depolarizations (SDs) also contribute to delayed cerebral ischemia and poor neurological outcome. This study seeks to explore the intermeasure correlation of different measures of CA, as well as correlation with SD and neurological outcome. Methods: Simultaneous measurement of 7 continuous indices of CA was calculated in 19 subjects entered in a prospective study of SD in aneurysmal subarachnoid hemorrhage undergoing surgical aneurysm clipping. Intermeasure agreement was assessed, and the association of each index with modified Rankin Scale score at 90 days and occurrence of SD was assessed. Results: There were 4102 hours of total monitoring time across the 19 subjects. In time-resolved assessment, no CA measures demonstrated significant correlation; however, most demonstrate significant correlation averaged over 1 hour. Pressure reactivity (PRx), oxygen reactivity, and oxygen saturation reactivity were significantly correlated with modified Rankin Scale score at 90 days. PRx and oxygen reactivity also were correlated with the occurrence of SD events. Across multiple CA measure reactivity indices, a threshold between 0.3 and 0.5 was most associated with intervals containing SD. Conclusions: Different continuous CA indices do not correlate well with each other on a highly time-resolved basis, so should not be viewed as interchangeable. PRx and oxygen reactivity are the most reliable indices in identifying risk of worse outcome in patients with aneurysmal subarachnoid hemorrhage undergoing surgical treatment. SD occurrence is correlated with impaired CA across multiple CA measurement techniques and may represent the pathological mechanism of delayed cerebral ischemia in patients with impaired CA. Optimization of CA in patients with aneurysmal subarachnoid hemorrhage may lead to decreased incidence of SD and improved neurological outcomes. Future studies are needed to evaluate these hypotheses and approaches.
Metabolic cross-feeding structures the assembly of polysaccharide degrading communities

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders structure the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical cross-feeding structure that allows biopolymer degraders to shape the dynamics of community assembly.
Cytogenetics to functional genomics: six decades journey of Professor P.K. Gupta

Summary We had the fortune of starting our scientific/research careers in the Molecular Biology and Crop Biotechnology Laboratory of Professor P.K. Gupta at Ch. Charan Singh University, Meerut, UP, India. Here, we describe the most important scientific contributions of our beloved mentor in the area of cytotaxonomy, cytogenetics, mutation breeding, quantitative genetics, molecular biology, crop biotechnology and plant genomics, on his 85th birthday. Important contributions made in the development and use of genomics resources including the development and use of different kinds of molecular markers, genetic and physical mapping, quantitative trait locus (QTL) interval mapping, genome‐wide association mapping and molecular breeding including marker‐assisted selection have been briefly summarized. Efforts have been also made to give readers a glimpse of important contributions in the study of cytology/apomixis of grasses, cytotaxonomic studies in asteraceae/fabaceae, nuclear/repetitive DNA content in Lolium, interspecific/intergeneric relationships involving the genus Hordeum and re‐examining taxonomy of the tribe Triticeae.
Parental support, marital conflict, and stress as predictors of depressive symptoms among African American adolescents

Given the increase of depressive symptoms among adolescents, it is essential to investigate familial and temperamental correlates of depressive symptoms such as parental support, marital conflict, and stress. Thus, using a cross-sectional design, the current study examined whether parental support, marital conflict, and stress predicted depressive symptoms. Then, using structural equation modeling, this study tested whether stress mediated the relationships among parental support, marital conflict, and depressive symptoms among African American adolescents while controlling for sex (N = 883). Results suggest that maternal support negatively related to depressive symptoms in contrast to stress and marital conflict. However, paternal support and sex were not statistically associated with depressive symptoms. Mediation results suggest that stress explained the relationships among parental support, marital conflict, and depressive symptoms. Family therapy and depression reduction implications are discussed.
Renin, aldosterone, the aldosterone-to-renin ratio, and incident hypertension among normotensive subjects from the general population

Abstract Aims To investigate the predictive ability of direct plasma renin and aldosterone concentrations as well as their ratio [aldosterone-to-renin (ARR)] for incident hypertension in the general population. Methods and results Concentration of renin and aldosterone were measured by a chemiluminescence immunoassay using the fully automated LIAISON® platform (DiaSorin) among 5362 participants of the population-based Gutenberg Health Study, who were normotensive and had no clinically overt cardiovascular disease at baseline. During a follow-up period of 5 years, 18.6% (n = 996) developed a new-onset hypertension. Comparing extreme quartiles of biomarker distribution, the relative risk (RR) for incident arterial hypertension was found to be 1.58 [95% confidence interval (CI) 1.25–2.00; P = 0.00015; Q1 vs. Q4ref] for renin; 1.29 (95% CI 1.05–1.59, P = 0.018; Q4 vs. Q1ref) for aldosterone and 1.70 (95% CI 1.33–2.12; P < 0.0001; Q4 vs. Q1ref) for ARR after multivariable adjustment in men. In females, only high ARR was independently predictive for incident hypertension over 5 years [RR 1.29 (95% CI 1.04–1.62); P = 0.024]. Even in the subgroup of individuals having biomarker concentrations within the reference range, high ARR was predictive for new-onset hypertension in men [RR 1.44 (95% CI 1.13–1.83); P = 0.003]. Finally, synergistic effects of co-prevalent obesity and ARR on incident hypertension were also demonstrated, resulting in markedly higher risk estimates as seen for biomarker alone [RR of 2.70 (95% CI 2.05–3.6) for Q4 of ARR and having body mass index ≥ 30 kg/m2 vs. low ARR (Q1ref) and normal weight; P < 0.0001]. Conclusion Among normotensives from the general population ARR possesses a stronger predictive value for incident hypertension than renin or aldosterone alone. The prediction of arterial hypertension by ARR was even stronger in obese subjects.
Different tumorigenicity and distinct metastasis and gene signature between orthotopic and subcutaneous neuroblastoma xenografted mice

Patient-derived (PDX) and cell-derived (CDX) xenograft models are widely used in preclinical studies of human neuroblastoma. In this study, we constructed orthotopic and subcutaneous neuroblastoma CDX models by injecting human neuroblastoma cells into the adrenal gland and the flanks of immunodeficient mice, respectively. The tumorigenesis, metastasis and response to chemotherapy for the two models were also compared. Our results indicated that orthotopic tumor mice showed significantly faster tumor growth than that of subcutaneous mice. Importantly, the expression of PHOX2B and GAB2 was dramatically increased in the tumors of orthotopic CDX mice. Furthermore, orthotopic CDX mice developed multiple organ metastasis resembling that of neuroblastoma patients, while metastasis occurred predominantly in lung in subcutaneous CDX mice. Moreover, the two CDX models showed comparable response to cyclophosphamide treatment. Our results suggest that orthotopic CDX mice are superior to subcutaneous CDX mice as a preclinical model to study human neuroblastoma.
Cryptic Metabolites from Marine-Derived Microorganisms Using OSMAC and Epigenetic Approaches

Marine microorganisms have proven to be a source of new natural products with a wide spectrum of biological activities relevant in different industrial sectors. The ever-increasing number of sequenced microbial genomes has highlighted a discrepancy between the number of gene clusters potentially encoding the production of natural products and the actual number of chemically characterized metabolites for a given microorganism. Homologous and heterologous expression of these biosynthetic genes, which are often silent under experimental laboratory culture conditions, may lead to the discovery of new cryptic natural products of medical and biotechnological interest. Several new genetic and cultivation-based strategies have been developed to meet this challenge. The OSMAC approach (one strain—many compounds), based on modification of growth conditions, has proven to be a powerful strategy for the discovery of new cryptic natural products. As a direct extension of this approach, the addition of chemical elicitors or epigenetic modifiers have also been used to activate silent genes. This review looks at the structures and biological activities of new cryptic metabolites from marine-derived microorganisms obtained using the OSMAC approach, the addition of chemical elicitors, and enzymatic inhibitors and epigenetic modifiers. It covers works published up to June 2021.
Assessment of Voltage Sags in Large Power Consumer Based on Monte Carlo Method

To assess and solve the voltage sag at user node, an approach of using Monte Carlo stochastic simulation method to evaluate the nodal voltage sag is proposed. The HyperSIM simulation tool is adopted to calculate and analyze the impacting degree of fault on voltage sag at user node under different probability models to decide the weak links of power network and thereby to offer thinking for both power network renovation and determination of installation position for the devices to remedy voltage sag. By means of the simulation of actual power system, the expected value of the magnitude of voltage sag at user node is obtained by calculation and the link that has the utmost impact on the voltage at user node is found. The proposed approach is available for reference in power network planning and scheduling.