Miracle-dz/UniFAR-FTUs huggingface dataset:
Local and generalized sensitization of thermally evoked defensive behavior in caterpillars

In addition to camouflage and chemical toxicity, many caterpillars defend themselves against predators with sudden sharp movements. For smaller species, these movements propel the body away from the threat, but in larger caterpillars, such as the tobacco hornworm, Manduca sexta, the movement is a defensive strike targeted to a noxious stimulus on the abdomen. Previously, strikes have been studied using mechanical stimulation like poking or pinching the insect, but such stimuli are hard to control. They also introduce mechanical perturbations that interfere with measurements of the behavior. We have now established that strike behavior can be evoked using infra‐red lasers to provide a highly localized and repeatable heat stimulus. The latency from the end of an effective stimulus to the start of head movement decreased with repeated stimuli and this effect generalized to other stimulus locations indicating a centrally mediated component of sensitization. The tendency to strike increased with two successive subthreshold stimuli. When delivered to different locations or to a single site, this split‐pulse stimulation revealed an additional site‐specific sensitization that has not previously been described in Manduca. Previous work shows that strong stimuli increases the effectiveness of sensory stimulation by activating a long‐lasting muscarinic cation current in motoneurons. Injection of muscarinic cholinergic antagonists, scopolamine methyl bromide or quinuclidinyl benzilate, only decreased the strike probability evoked by paired stimuli at two locations and not at a single site. This strongly suggests a role of muscarinic acetylcholine receptors in the generalized sensitization of nociceptive responses in caterpillars.
Intratumoral CD8+ T cells with stem cell–like properties: Implications for cancer immunotherapy

Intratumoral PD-1+ TCF1+ CD8+ T cells with stem cell–like properties mediate cellular expansion and tumor control in response to immunotherapy. Intratumoral PD-1+ TCF1+ CD8+ T cells with stem cell–like properties mediate cellular expansion and tumor control in response to immunotherapy.
Long non coding RNA H19: An emerging therapeutic target in fibrosing diseases

Abstract Fibrosis is characterised by excessive deposition of the extracellular matrix (ECM) and develops because of fibroblast differentiation during the process of inflammation. There are few effective treatment options for this diseases due to the aetiology of fibrosis is not completely clarified. Long non-coding RNAs (lncRNAs), a type of ncRNA with a length of greater than 200 nucleotides without evident protein coding function, are important regulators of most biological and pathological processes, including participation, regulation or mediation of disease development. Among them, H19 is recently discovered as a class of lncRNAs which is related to fibrotic disease and inflammation. These observations implied a potential role for H19 as a promising therapeutic targets for treatment of fibrotic diseases. In this review, we will describe the characteristics of H19 and summarise recent advances in the mechanisms of H19 in the process of fibrosis. Finally, we will succinctly discuss the recent progress of the involvement of H19 in the development and pathogenesis of fibrosis diseases.
Quantifying how changing mangrove cover affects ecosystem carbon storage in coastal wetlands.

Despite overall global declines, mangroves are expanding into and within many subtropical wetlands, leading to heterogeneous cover of marsh-mangrove coastal vegetation communities near the poleward edge of mangroves' ranges. Coastal wetlands are globally important carbon sinks, yet the effects of shifts in mangrove cover on organic carbon (OC) storage remains uncertain. We experimentally maintained black mangrove (Avicennia germinans) or marsh vegetation in patches (n = 1120, 3 × 3 m) along a gradient in mangrove cover (0-100%) within coastal wetland plots (n = 10, 24 × 42 m) and measured changes in OC stocks and fluxes. Within patches, above and belowground biomass (OC) was 1630% and 61% greater for mangroves than for recolonized marshes, and soil OC was 30% greater beneath mangrove than marsh vegetation. At the plot scale, above and belowground biomass increased linearly with mangrove cover but soil OC was highly variable and unrelated to mangrove cover. Root ingrowth was not different in mangrove or marsh patches, nor did it change with mangrove cover. After 11 months, surface OC accretion was negatively related to plot-scale mangrove cover following a high-wrack deposition period. However, after 22 months, accretion was 54% higher in mangrove patches, and there was no relationship to plot-scale mangrove cover. Marsh (Batis maritima) leaf and root litter had 1000% and 35% faster breakdown rates (k) than mangrove (A. germinans) leaf and root litter. Soil temperatures beneath mangroves were 1. 4ºC lower, decreasing aboveground k of fast- (cellulose) and slow-decomposing (wood) standard substrates. Wood k in shallow soil (0-15 cm) was higher in mangrove than marsh patches, but vegetation identity did not impact k in deeper soil (15-30 cm). We found that mangrove cover enhanced OC storage by increasing biomass, creating more recalcitrant organic matter and reducing k on the soil surface by altering microclimate, despite increasing wood k belowground and decreasing allochthonous OC subsidies. Our results illustrate the importance of mangroves in maintaining coastal OC storage, but also indicate that the impacts of vegetation change on OC storage may vary based on ecosystem conditions, organic matter sources, and the relative spatio-temporal scales of mangrove vegetation change.
A 21-bp indel within the LLGL1 gene is significantly associated with litter size in goat

Abstract The scribble cell polarity complex component (LLGL1) is part of the cytoskeletal network and is involved in maintaining cell polarity and epithelial integrity. Based on the whole-genome sequencing analysis in goat, LLGL1 gene is suggested as a putative important candidate gene affecting litter size in Shaanbei White Cashmere Goats (SBWC). Therefore, the objective of this study was to uncover the possible novel insertion/deletion (Indel) variant in goat LLGL1 gene and to evaluate its association with litter size of SBWC (n = 827). Using the PCR detection and DNA sequencing, the 21-bp indel in the upstream of LLGL1 was firstly founded and two genotypes were identified: II (insertion/insertion) and ID (insertion/deletion), respectively. Association analyses revealed that the 21-bp indel was significantly correlated with litter size (p = 0.017). Notably, the individuals with II genotype were significantly greater than that of the genotype ID, and the ‘I’ allele was dominant. Additionally, the remarkable influence of the indel on traits might be related to the change of DEAF-1-related (NUDR) binding site through bioinformatics analysis. Briefly, the 21-bp indel within the goat LLGL1 gene could be an effective DNA molecular marker and provide valuable theoretical basis for marker-assisted selection (MAS) in goat industry.
Characterization of the immunomodulatory and anti-Helicobacter pylori properties of the human gastric isolate Lactobacillus rhamnosus UCO-25A

Abstract The ability to form biofilms and the potential immunomodulatory properties of the human gastric isolate Lactobacillus rhamnosus UCO-25A were characterized in vitro. It was demonstrated that L. rhamnosus UCO-25A is able to form biofilms on abiotic and cell surfaces, and to modulate the inflammatory response triggered by Helicobacter pylori infection in gastric epithelial cells and THP-1 macrophages. L. rhamnosus UCO-25A exhibited a substantial anti-inflammatory effect in both cell lines and improved IL-10 levels produced by challenged macrophages. Additionally, UCO-25A protected AGS cells against H. pylori infection with a higher pathogen inhibition when a biofilm was formed. Given the importance of inflammation in H. pylori-mediated diseases, the differential modulation of the inflammatory response in the gastric mucosa by an autochthonous strain is an attractive alternative for improving H. pylori eradication and reducing the severity of the diseases that arise from the resulting chronic inflammation.
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Abstract Microbiology depends on the availability of annotated microbial genomes for many applications. Comparative genomics approaches have been a major advance, but consistent and accurate annotations of genomes can be hard to obtain. In addition, newer concepts such as the pan-genome concept are still being implemented to help answer biological questions. Hence, we present proGenomes2, which provides 87 920 high-quality genomes in a user-friendly and interactive manner. Genome sequences and annotations can be retrieved individually or by taxonomic clade. Every genome in the database has been assigned to a species cluster and most genomes could be accurately assigned to one or multiple habitats. In addition, general functional annotations and specific annotations of antibiotic resistance genes and single nucleotide variants are provided. In short, proGenomes2 provides threefold more genomes, enhanced habitat annotations, updated taxonomic and functional annotation and improved linkage to the NCBI BioSample database. The database is available at http://progenomes.embl. de/.
Nanoparticles and Vaccine Development.

In spite of the progress of conventional vaccines, improvements are required due to concerns about the low immunogenicity of these vaccines, toxicity, instability, and the need for multiple administrations. To overcome mentioned problems, nanotechnology have recently been incorporated into vaccine development. Nanotechnology increasingly plays an important role in vaccine development Nanocarrier-based delivery systems offer an opportunity to increase the cellular and humoral immune responses. The use of nanoparticles in vaccine formulations allows not only enhanced immunogenicity and stability of antigen, but also targeted delivery and slow release. Over the past decade nanoscale size materials such as virus-like particles, liposomes, ISCOMs, polymeric, inorganic nanoparticles and emulsions have received attention as potential delivery vehicles for vaccine antigens which can both stabilize vaccine antigens and act as adjuvants. This advantage is attributable to the nanoscale particle size, which facilitates uptake by antigen presenting cells (APCs) then leading to efficient antigen recognition and presentation. Modifying the surfaces of nanoparticles with a different of targeting moieties permits the delivery of antigens to specific receptors on the cell surface, thereby stimulating selective and specific immune responses. This review provides an overview of recent advances in nanovaccinology.
Abnormal Activity of Neck Inspiratory Muscle During Sleep as a Prognostic Indicator in COPD.

RATIONALE In patients with chronic obstructive pulmonary disease (COPD), increased activity of neck inspiratory muscles has been reported as a compensatory response to hyperinflation-related diaphragmatic dysfunction. The persistence of this activity during sleep could attenuate sleep-related hypoventilation, but also negatively impact sleep and clinical outcomes. OBJECTIVES To assess the persistence of neck muscle activity during sleep in COPD patients recovering from severe exacerbations (i.e. requiring hospitalization), and its impact on sleep quality and recurrence of exacerbation. METHODS Video-polysomnography with neck muscles electromyogram was performed in COPD patients recovering from severe exacerbation. The follow-up period lasted 6 months to record the next severe exacerbation. RESULTS Twenty-six out of 29 patients included (median [25th-75th] age of 71 [64-72] years, 55% male, body mass index of 24 [21-29], % predicted forced expiratory volume in the first second of expiration of 37 [29-45], and BODE index 6 [5-7]), exhibited sleep-related neck muscles activity, which was intermittent (limited to N3 sleep) in 17 and permanent throughout sleep in 9. Alpha-delta electroencephalographic activity during N3 sleep was observed in 87% of patients. Compared to patients with no or intermittent neck muscle activity, those with permanent neck muscle activity showed more disrupted sleep, had experienced more exacerbations in the previous year, and suffered their next severe exacerbation earlier. CONCLUSIONS Sleep-related neck muscle activity during sleep is frequent in COPD patients recovering from severe exacerbation and seems to negatively affect sleep quality and prognosis, thus its identification might improve COPD management after severe exacerbation.
A rapid triage test for active pulmonary tuberculosis in adult patients with persistent cough

A blood protein signature discriminates active tuberculosis (TB) from other TB-like disease in adults regardless of HIV status. A triage test for tuberculosis Tuberculosis remains a global health burden. Ahmad et al. used machine learning to develop an algorithm that distinguished active tuberculosis from other diseases with similar symptoms by measuring expression of four proteins in blood samples. The authors validated their triage test’s discriminatory power using blood samples from subjects with persistent cough across several continents, showing that performance was improved when detection of antibodies against a mycobacterial antigen was added to the panel. These promising results support further development and field testing using a point-of-care format. Improved tuberculosis (TB) prevention and control depend critically on the development of a simple, readily accessible rapid triage test to stratify TB risk. We hypothesized that a blood protein-based host response signature for active TB (ATB) could distinguish it from other TB-like disease (OTD) in adult patients with persistent cough, thereby providing a foundation for a point-of-care (POC) triage test for ATB. Three adult cohorts consisting of ATB suspects were recruited. A bead-based immunoassay and machine learning algorithms identified a panel of four host blood proteins, interleukin-6 (IL-6), IL-8, IL-18, and vascular endothelial growth factor (VEGF), that distinguished ATB from OTD. An ultrasensitive POC-amenable single-molecule array (Simoa) panel was configured, and the ATB diagnostic algorithm underwent blind validation in an independent, multinational cohort in which ATB was distinguished from OTD with receiver operator characteristic–area under the curve (ROC-AUC) of 0.80 [95% confidence interval (CI), 0.75 to 0.85], 80% sensitivity (95% CI, 73 to 85%), and 65% specificity (95% CI, 57 to 71%). When host antibodies against TB antigen Ag85B were added to the panel, performance improved to 86% sensitivity and 69% specificity. A blood-based host response panel consisting of four proteins and antibodies to one TB antigen can help to differentiate ATB from other causes of persistent cough in patients with and without HIV infection from Africa, Asia, and South America. Performance characteristics approach World Health Organization (WHO) target product profile accuracy requirements and may provide the foundation for an urgently needed blood-based POC TB triage test.
Comment on “Prognostic and predictive implications of sarcopenia in Western patients undergoing gastric resections for carcinoma of the stomach”

To the Editor, We have recently read with great interest the article by Sierzega et al titled “Prognostic and predictive implications of sarcopenia in Western patients undergoing gastric resections for carcinoma of the stomach. ” They determined that sarcopenia, defined by skeletal muscle index, is associated with an increased risk of postoperative morbidity and impaired long‐term survival. We found these results particularly important as the authors reported that there were few reports on the role of sarcopenia in patients with gastric cancer, and those published were derived mostly from countries outside Europe and America. However, before discussing the current results, we would like to direct the attention of readers to some methodological issues. First, the study reported the results of stomach resections in patients with gastric adenocarcinoma between 2012 and 2015. This protocol was designed as a retrospective, long‐term, follow‐up study of patients who were scanned with computed tomography (CT). This point is critical because of the alteration of attenuation between individual scanners, which might readily affect the current results. Therefore, Sierzega et al should clarify whether all image analyses of CT scans reported in the study were observed from one or more CT scanners. Second, in 2010, the European Working Group on Sarcopenia in Older People (EWGSOP) defined sarcopenia based on the measurement of muscle mass and function. Furthermore, in 2018, the working group met again (EWGSOP2), and according to the revised report, muscle strength came to the forefront as it was recognized that muscle strength was better than muscle mass in predicting adverse outcomes. According to EWGSOP and EWGSOP2 criteria, the definition of sarcopenia in this article seems to be suboptimal because the muscle strength of patients was not reported, and patients were classified solely based on the measurement of muscle mass. We believe that the impact of such a potential incidence of misclassification on the results should be considered as it might help to generate results in clinical practice. Further studies should be designed considering these points.
The RNA polymerase III repressor MAF1 is regulated by ubiquitin-dependent proteasome degradation and modulates cancer drug resistance and apoptosis

MAF1 homolog, negative regulator of RNA polymerase III (MAF1) is a key repressor of RNA polymerase (pol) III–dependent transcription and functions as a tumor suppressor. Its expression is frequently down-regulated in primary human hepatocellular carcinomas (HCCs). However, this reduction in MAF1 protein levels does not correlate with its transcript levels, indicating that MAF1 is regulated post-transcriptionally. Here, we demonstrate that MAF1 is a labile protein whose levels are regulated through the ubiquitin-dependent proteasome pathway. We found that MAF1 ubiquitination is enhanced upon mTOR complex 1 (TORC1)–mediated phosphorylation at Ser-75. Moreover, we observed that the E3 ubiquitin ligase cullin 2 (CUL2) critically regulates MAF1 ubiquitination and controls its stability and subsequent RNA pol III–dependent transcription. Analysis of the phenotypic consequences of modulating either CUL2 or MAF1 protein expression revealed changes in actin cytoskeleton reorganization and altered sensitivity to doxorubicin-induced apoptosis. Repression of RNA pol III–dependent transcription by chemical inhibition or knockdown of BRF1 RNA pol III transcription initiation factor subunit (BRF1) enhanced HCC cell sensitivity to doxorubicin, suggesting that MAF1 regulates doxorubicin resistance in HCC by controlling RNA pol III–dependent transcription. Together, our results identify the ubiquitin proteasome pathway and CUL2 as important regulators of MAF1 levels. They suggest that decreases in MAF1 protein underlie chemoresistance in HCC and perhaps other cancers and point to an important role for MAF1 and RNA pol III–mediated transcription in chemosensitivity and apoptosis.
A Software-Defined Radio Receiver for Wireless Recording From Freely Behaving Animals

To eliminate tethering effects on the small animals’ behavior during electrophysiology experiments, such as neural interfacing, a robust and wideband wireless data link is needed for communicating with the implanted sensing elements without blind spots. We present a software-defined radio (SDR) based scalable data acquisition system, which can be programmed to provide coverage over standard-sized or customized experimental arenas. The incoming RF signal with the highest power among SDRs is selected in real-time to prevent data loss in the presence of spatial and angular misalignments between the transmitter (Tx) and receiver (Rx) antennas. A 32-channel wireless neural recording system-on-a-chip (SoC), known as WINeRS-8, is embedded in a headstage and transmits digitalized raw neural signals, which are sampled at 25 kHz/ch, at 9 Mbps via on-off keying (OOK) of a 434 MHz RF carrier. Measurement results show that the dual-SDR Rx system reduces the packet loss down to 0.12%, on average, by eliminating the blind spots caused by the moving Tx directionality. The system operation is verified in vivo on a freely behaving rat and compared with a commercial hardwired system.
Effects of synthetic (JWH-018) cannabinoids treatment on spermatogenesis and sperm function

Abstract JWH-018 is a synthetic cannabinoid which has been increasingly used by adolescents and adults, and is known to cause severe multi-organ failure. However, little is known about the complications and toxicological effects of JWH-018 on reproduction system. Therefore, the aim of the present study is to investigate the effects of JWH-018 on testis and spermatogenesis. Thirty CD-1 male rats were distributed into six groups, control group (C1 and C2), ethanol group (E1 and E2), and JWH-018 group (JWH1 and JWH2), which were administered 0.9% NaCl, %100 ethanol, and JWH-018 (0.3 mg/kg) respectively for 9 d. We euthanized C1, E1, and JWH1 group mice at day 2 and C2, E2, and JWH2 group mice at 45 d after the last injection to evaluate the acute testis damage and potential recovery of spermatogenesis. The histopathology of seminiferous epithelium was evaluated and organ weight, sperm concentration and motility, membrane integrity, and serum testosterone levels were statistically analyzed. In JWH1, seminiferous tubule degeneration, partial germ cell depletion disorganized seminiferous epitheliums were seen. We also observed significantly decreased sperm concentration, sperm motility, intact membrane, and testosterone levels in JWH1 group compared to other groups. Forty-five days after the JWH-018 treatment, sperm concentration, motility, and testosterone level were increased, suggesting that testis and spermatogenesis can recover. We concluded that the use of JWH-018 may adversely affect male reproductive potential and testis histopathology.