Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale

Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013; Daly et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with 13C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and 15N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of 13C and 15N incorporation in individual cells, while isotope ratio monitoring–gas chromatography–mass spectrometry (IRM–GC–MS) was used to measure 13CO2, and 13CH4 as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. 13CO2 production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia. The primary genera detected in the incubations, Halanaerobium and Fusibacter, are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.
From Social Networks to Publishing Platforms: A Review of the History and Scholarship of Academic Social Network Sites

Social network sites enable people to easily connect to and communicate with others. Following the success of generic platforms such as Facebook, a variety of online services launched during the mid 2000s in order to bring the benefits of online social networking to an academic audience. However, it is not clear whether these academic social network sites (ASNS) are primarily aligned with social networking or alternative publishing, and functionalities continue to change. Now ten years since the launch of the three main platforms which currently lead the market (Academia.edu, ResearchGate, and Mendeley), it is timely to review how and why ASNS are used. This paper discusses the history and definition of ASNS, before providing a comprehensive review of the empirical research related to ASNS to-date. Five main themes within the research literature are identified, including: the relationship of the platforms to Open Access publishing; metrics; interactions with others through the platforms; platform demographics and social structure; and user perspectives. Discussing the themes in the research both provides academics with a greater understanding of what ASNS can do and their limitations, and identifies gaps in the literature which would be valuable to explore in future research.
Diving Behavior and Fine-Scale Kinematics of Free-Ranging Risso's Dolphins Foraging in Shallow and Deep-Water Habitats

Air-breathing marine predators must balance the conflicting demands of oxygen conservation during breath-hold and the cost of diving and locomotion to capture prey. However, it remains poorly understood how predators modulate foraging performance when feeding at different depths and in response to changes in prey distribution and type. Here, we used high-resolution multi-sensor tags attached to Risso’s dolphins (Grampus griseus) and concurrent prey surveys to quantify their foraging performance over a range of depths and prey types. Dolphins (N=33) foraged in shallow and deep habitats [seabed depths less or more than 560m, respectively] and within the deep habitat, in vertically stratified prey features occurring at several aggregation levels. Generalized linear mixed-effects models indicated that dive kinematics were driven by foraging depth rather than habitat. Bottom-phase duration and number of buzzes (attempts to capture prey) per dive increased with depth. In deep dives, dolphins were gliding for >50% of descent and adopted higher pitch angles both during descent and ascents, which was likely to reduce energetic cost of longer transits. This lower cost of transit was counteracted by the record of highest vertical swim speeds, rolling maneuvers and stroke rates at depth, together with a 4-fold increase in the inter-buzz interval, suggesting higher costs of pursuing and handling prey compared to shallow-water feeding. In spite of the increased capture effort at depth, dolphins managed to keep their estimated overall metabolic rate comparable across dive types. This indicates that adjustments in swimming modes may enable energy balance in deeper dives. If we think of the surface as a central place where divers return to breathe, our data match predictions that central place foragers should increase the number and likely quality of prey items at greater distances. These dolphins forage efficiently from near-shore benthic communities to depth-stratified scattering layers, enabling them to maximize their fitness.
Tonic exploration governs both flexibility and lapses

In many cognitive tasks, lapses (spontaneous errors) are tacitly dismissed as the result of nuisance processes like sensorimotor noise, fatigue, or disengagement. However, some lapses could also be caused by exploratory noise: randomness in behavior that facilitates learning in changing environments. If so, then strategic processes would need only up-regulate (rather than generate) exploration to adapt to a changing environment. This view predicts that more frequent lapses should be associated with greater flexibility because these behaviors share a common cause. Here, we report that when rhesus macaques performed a set-shifting task, lapse rates were negatively correlated with perseverative error frequency across sessions, consistent with a common basis in exploration. The results could not be explained by local failures to learn. Furthermore, chronic exposure to cocaine, which is known to impair cognitive flexibility, did increase perseverative errors, but, surprisingly, also improved overall set-shifting task performance by reducing lapse rates. We reconcile these results with a state-switching model in which cocaine decreases exploration by deepening attractor basins corresponding to rule states. These results support the idea that exploratory noise contributes to lapses, affecting rule-based decision-making even when it has no strategic value, and suggest that one key mechanism for regulating exploration may be the depth of rule states.
Freezing Facilitates Formation of Silver Nanoparticles under Natural and Simulated Sunlight Conditions.

Freezing is essential in the light-mediated transformation of organic pollutants. However, the effects of the freezing process on the reduction of Ag+ by natural organic matter (NOM) remains unclear, causing significant uncertainties in the natural formation of silver nanoparticles (AgNPs). This study investigated the sunlight-induced reduction of Ag+ by NOM under natural or controlled freezing processes. Natural (outdoor) freezing experiments demonstrated intense aggregation and precipitation of AgNPs in three aqueous media including a NOM solution and two river waters, under natural sunlight irradiation. Indoor experiments under simulated sunlight irradiation and controlled freezing processes showed that freezing at -20 °C and repeated freeze-thaw cycles (-20 °C to 4 °C) drastically accelerated the formation and growth of AgNPs compared to maintenance at 4 °C. Finally, under the natural freezing process, commercial AgNPs were found to influence the redox reduction of Ag+ probably through a reduction in dissolution rates and homoaggregation with AgNP newly formed in the river water samples. Additionally, the enhancement effect of freezing on AgNPs formation was confirmed in the presence of Ag+ and AgNPs both at environmentally relevant concentration levels, especially upon light irradiation. This work emphasizes the importance of freezing processes on the natural formation of AgNPs.
Liar! Liar! (when stakes are higher): Understanding how the overclaiming technique can be used to measure faking in personnel selection.

Overclaiming questionnaires (OCQs), which capture overclaiming behavior, or exaggerating one's knowledge about a given topic, have been proposed as potentially indicative of faking behaviors that plague self-report assessments in job application settings. The empirical evidence on the efficacy of OCQs in this respect is inconsistent, however. We draw from expectancy theory to reconcile these inconsistencies and identify the conditions under which overclaiming behavior will be most indicative of faking. We propose that the assessment context must be tied to an outcome with high valence, and that the content of the OCQ must match the perceived knowledge requirements of the target job, such that overclaiming knowledge of that content will be instrumental to receiving a job offer. We test these propositions through three studies. First, in a sample of 519 applicants to firefighter positions, we demonstrate that overclaiming on a job-relevant OCQ is positively associated with other indicators of faking and self-presentation. Next, we demonstrate through a repeated-measures experiment (N = 252) that participants in a simulated personnel selection setting overclaim more knowledge on a job-relevant OCQ than on a job-irrelevant OCQ, compared with when they are instructed to respond honestly. Finally, in a novel repeated-measures personnel selection paradigm (N = 259), we observed more overclaiming during a selection assessment compared with a research assessment, and we observed that this job-application overclaiming behavior predicted deviant behavior following selection. Altogether, the results show that overclaiming behavior is most indicative of faking in job application assessments when an OCQ contains job-relevant (rather than job-irrelevant) content. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Follicular T helper cells shape the HCV-specific CD4 T cell repertoire after viral elimination.

BACKGROUND Chronic HCV-infection is characterized by a severe impairment of HCV-specific CD4 T cell help that is driven by chronic antigen stimulation. We aimed to study the fate of HCV-specific CD4 T cells after viral elimination. METHODS HCV-specific CD4 T cell responses were longitudinally analyzed using MHC class II tetramer-technology, multicolor flow cytometry and RNA sequencing in a cohort of chronically HCV-infected patients undergoing therapy with direct-acting antivirals. In addition, HCV-specific neutralizing antibodies and CXCL13 levels were analyzed. RESULTS We observed that the frequency of HCV-specific CD4 T cells increased within two weeks after initiation of DAA therapy. Multicolor flow cytometry revealed a downregulation of exhaustion and activation markers and an upregulation of memory-associated markers. While cells with a Th1 phenotype were the predominant subset at baseline, cells with phenotypic and transcriptional characteristics of follicular T helper cells increasingly shaped the circulating HCV-specific CD4 T cell repertoire, suggesting antigen-independent survival of this subset. These changes were accompanied by a decline of HCV-specific neutralizing antibodies and the germinal center activity. CONCLUSION We identified a population of HCV-specific CD4 T cells with a follicular T helper cell signature that is maintained after therapy-induced elimination of persistent infection and may constitute an important target population for vaccination efforts to prevent re-infection and immunotherapeutic approaches for persistent viral infections.
Apo lipoprotein E4 gene APOE4: An early predictor of Dementia / Alzheimer's disease

The present study aimed to determine the relationship of APOE4 with socio demographic variables as well as with co-morbidities including hypertension and diabetes mellitus. In this study, 200 subjects with dementia were recruited, out of these 200 patients APOE4 was present in 130 cases, 85 (65.4%) were male and 45 (34.6%) females. However, in 70 cases APOE4 was missing, 41 (58.6%) males and 29 (41.4%) were females. Subjects who showed absence of APOE4 were considered as control. Educational level and socioeconomic status were categorized as low, middle and high. BMI was considered as low or normal according to the standard criteria. 10 ml venous blood was obtained for genomic DNA extraction and genotyping for the Apo lipoprotein E (APOE) alleles using standard methods. A high percentage of patients with cognitive disorder showed the presence of APOE4. Among these patients males were more suffered than females. Quantitative characteristics showed that with increasing age the percentage of APOE4 was increased, however, no effect on BMI was observed compared with the presence or absence of APOE4. A direct relationship of APOE4 with diabetes was observed. In conclusion, presence of APOE4 in male patients with cognitive disorder may increase the risk of dementia/Alzheimer’s disease with middle socioeconomic status and education as well as diabetes. However no effect of BMI and blood pressure was observed.
Traditional Chinese Medicine Prolongs Progression-Free Survival and Enhances Therapeutic Effects in Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor (EGFR-TKI)Treated Non-Small-Cell Lung Cancer (NSCLC) Patients Harboring EGFR Mutations

Background Lung cancer is the most common cause of cancer-associated deaths worldwide. This study aimed to investigate the efficacy and safety of Traditional Chinese Medicine combining EGFR-TKIs in treatment of NSCLC patients harboring EGFR mutations. Material/Methods This study involved 153 advanced-stage NSCLC patients harboring EGFR mutations. Patients were divided into a Control group (administered EGFR-TKI, n=61) and an Experimental group (administered Traditional Chinese Medicine combining EGFR and TKI, n=92). Progression-free survival (PFS) was evaluated for exon 19 deletion and/or 21 deletion patients. Disease control rate (DCR) was assessed to observe therapeutic effects. Adverse effects, including rashes, diarrhea, ALT/AST increase, dental ulcers, and onychia lateralis, were also evaluated. Results TCM combining EGFR-TKI (90.11%) demonstrated no DCR improvement compared to single EGFR-TKI (83.33%) (p>0.05). Median PFS (mPFS) of TCM combining EGFR-TKI (13 months) was significantly longer compared to that in the single EGFR-TKI group (8.8 months) (p=0.001). For 19DEL mutant NSCLC, the mPFS (11 months) in TCM combining EGFR-TKI was significantly longer compared to single EGFR-TKI (8.5 months) (p=0.007). The mPFS of L858 mutant NSCLC patients in EGFR-TKI combining CTM (14 months) was significantly longer compared to single EGFR-TKI (9.5 months) (p=0.015). TCM combining EGFR-TKI was more inclined to prolong mPFS of NSCLC with exon 21 deletion. TCM combining EGFR-TKI illustrated no additional adverse effects in NSCLC patients (p=0.956). Conclusions Application of Traditional Chinese Medicine prolonged progression-free survival and enhanced therapeutic effect in NSCLC patients harboring EGFR mutations receiving EGFR-TKI treatment. Meanwhile, adjunctive Chinese medicine combining EGFR-TKI in NSCLC with EGFR mutations caused no adverse effects.
Bartonella rochalimae, B. grahamii, B. elizabethae, and Wolbachia spp. in Fleas from Wild Rodents near the China-Kazakhstan Border

The Alataw Pass, near the Ebinur Lake Wetland (northwest of China) and Taldykorgan (east of Kazakhstan), is a natural habitat for wild rodents. To date, little has been done on the surveillance of Bartonella spp. and Wolbachia spp. from fleas in the region. Here we molecularly detected Bartonella spp. and Wolbachia spp. in wild rodent fleas during January and October of 2016 along the Alataw Pass-Kazakhstan border. A total of 1,706 fleas belonging to 10 species were collected from 6 rodent species. Among the 10 flea species, 4 were found to be positive for Wolbachia, and 5 flea species were positive for Bartonella. Molecular analysis indicated that i) B. rochalimae was firstly identified in Xenopsylla gerbilli minax and X. conforms conforms, ii) B. grahamii was firstly identified in X. gerbilli minax, and iii) B. elizabethae was firstly detected in Coptopsylla lamellifer ardua, Paradoxopsyllus repandus, and Nosopsyllus laeviceps laeviceps. Additionally, 3 Wolbachia endosymbionts were firstly found in X. gerbilli minax, X. conforms conforms, P. repandus, and N. laeviceps laeviceps. BLASTn analysis indicated 3 Bartonella species showed genotypic variation. Phylogenetic analysis revealed 3 Wolbachia endosymbionts were clustered into the non-Siphonaptera Wolbachia group. These findings extend our knowledge of the geographical distribution and carriers of B. rochalimae, B. grahamii, B. elizabethae, and Wolbachia spp. In the future, there is a need for China-Kazakhstan cooperation to strengthen the surveillance of flea-borne pathogens in wildlife.
Brentuximab vedotin in the treatment of CD30-positive PTCL.

The development of Brentuximab vedotin has opened a new era in the management of PTCL. The improved outcomes with BV-CHP versus CHOP in the ECHELON-2 trial are practice changing for common nodal CD30+ PTCLs. Questions regarding the optimal cut off of CD30 expression for BV-CHP therapy and the efficacy and safety of BV-CHP in less common subtypes of CD30+ PTCL subtypes await clarification.
The Positive Allosteric Modulator of α2/3-Containing GABAA Receptors, KRM-II-81, Is Active in Pharmaco-Resistant Models of Epilepsy and Reduces Hyperexcitability after Traumatic Brain Injury

The imidizodiazepine, 5-(8-ethynyl-6-(pyridin-2-yl)-4H-benzo[f]imidazo[1,5-a][1,4]diazepin-3-yl)oxazole (KRM-II-81), is selective for α2/3-containing GABAA receptors. KRM-II-81 dampens seizure activity in rodent models with enhanced efficacy and reduced motor-impairment compared with diazepam. In the present study, KRM-II-81 was studied in assays designed to detect antiepileptics with improved chances of impacting pharmaco-resistant epilepsies. The potential for reducing neural hyperactivity weeks after traumatic brain injury was also studied. KRM-II-81 suppressed convulsions in corneal-kindled mice. Mice with kainate-induced mesial temporal lobe seizures exhibited spontaneous recurrent hippocampal paroxysmal discharges that were significantly reduced by KRM-II-81 (15 mg/kg, orally). KRM-II-81 also decreased convulsions in rats undergoing amygdala kindling in the presence of lamotrigine (lamotrigine-insensitive model) (ED50 = 19 mg/kg, i.p.). KRM-II-81 reduced focal and generalized seizures in a kainate-induced chronic epilepsy model in rats (20 mg/kg, i.p., three times per day). In mice with damage to the left cerebral cortex by controlled-cortical impact, enduring neuronal hyperactivity was dampened by KRM-II-81 (10 mg/kg, i.p.) as observed through in vivo two-photon imaging of layer II/III pyramidal neurons in GCaMP6-expressing transgenic mice. No notable side effects emerged up to doses of 300 mg/kg KRM-II-81. Molecular modeling studies were conducted: docking in the binding site of the α1β3γ2L GABAA receptor showed that replacing the C8 chlorine atom of alprazolam with the acetylene of KRM-II-81 led to loss of the key interaction with α1His102, providing a structural rationale for its low affinity for α1-containing GABAA receptors compared with benzodiazepines such as alprazolam. Overall, these findings predict that KRM-II-81 has improved therapeutic potential for epilepsy and post-traumatic epilepsy. SIGNIFICANCE STATEMENT We describe the effects of a relatively new orally bioavailable small molecule in rodent models of pharmaco-resistant epilepsy and traumatic brain injury. KRM-II-81 is more potent and generally more efficacious than standard-of-care antiepileptics. In silico docking experiments begin to describe the structural basis for the relative lack of motor impairment induced by KRM-II-81. KRM-II-81 has unique structural and anticonvulsant effects, predicting its potential as an improved antiepileptic drug and novel therapy for post-traumatic epilepsy.
miR-27a regulates vascular remodeling by targeting endothelial cells' apoptosis and interaction with vascular smooth muscle cells in aortic dissection

Rationale: Aortic dissection (AD) is caused by functional disorder of cells in the aortic wall, which is largely attributed to vascular remodeling. Therapeutic strategies for AD remain limited due to our incomplete understanding of the role of endothelial cells (ECs) in AD pathogenesis. This study aimed to identify the regulatory role of miR-27a in AD and provide a mechanistic basis for a non-invasive treatment of AD. Methods: We harvested aortas from normal and AD patients to explore the expression of miR-27a. In vitro and in vivo assays were preformed to explore the biological effects of differential expression of miR-27a in ECs and its regulatory effect on AD. Results: MiR-27a was lower in intima of AD samples than in healthy individuals. Downregulation of miR-27a in EC was due to up-regulated expression of fas-associated protein with death domain (FADD) and the activation of apoptosis pathway, which led to apoptosis of ECs. Migration of vascular smooth muscle cells was promoted by EC after downregulation of miR-27a due to enhancement of growth/differentiation factor 8 (GDF8) and repression of matrix metalloproteinase-20 (MMP20) in the co-culture system supernatants. Increase in FADD and apoptosis of ECs to induce AD was shown using mouse models of AD in which miR-27a was stably knocked-down by antagomir. Up-regulation of miR-27a by agomir led to a protective effect on AD. Conclusion: Treatment with miR-27a activator that targets apoptosis of ECs strongly diminished occurrence of AD, providing a new strategy for this disease.