Miracle-dz/UniFAR-FTUs huggingface dataset:
The Roles of Suspension-Feeding and Flux-Feeding Zooplankton as Gatekeepers of Particle Flux Into the Mesopelagic Ocean in the Northeast Pacific

Zooplankton are important consumers of sinking particles in the ocean’s twilight zone. However, the impact of different taxa depends on their feeding mode. In contrast to typical suspension-feeding zooplankton, flux-feeding taxa preferentially consume rapidly-sinking particles that would otherwise penetrate into the deep ocean. To quantify the potential impact of two flux-feeding zooplankton taxa (Aulosphaeridae [Rhizaria], and Limacina helicina [euthecosome pteropod]) and the total suspension-feeding zooplankton community, we measured depth-stratified abundances of these organisms during six cruises in the California Current Ecosystem. Using allometric-scaling relationships, we computed the percentage of carbon flux intercepted by flux feeders and suspension feeders. These estimates were compared to direct measurements of carbon flux attenuation made using drifting sediment traps and 238U-234Th disequilibrium. We found that carbon flux attenuation in the shallow twilight zone typically ranged from 500 – 1000 µmol organic C flux remineralized per 10-m vertical depth bin. This equated to approximately 6 – 10% of carbon flux remineralized / 10 m. The two flux-feeding taxa considered in this study could account for a substantial proportion of this flux near the base of the euphotic zone. The mean flux attenuation attributable to Aulosphaeridae was 0.69% / 10 m (median = 0.21%/10 m, interquartile range = 0.04 – 0.81%) at their depth of maximum abundance (~100 m), which would equate to ~ 10% of total flux attenuation in this depth range. The maximum flux attenuation attributable to Aulosphaeridae reached 4.2% / 10 m when these protists were most abundant. L. helicina, meanwhile, could intercept 0.45 – 1.6% of carbon flux / 10 m, which was slightly greater (on average) than the Aulosphaeridae. In contrast, suspension-feeding zooplankton in the mesopelagic (including copepods, euphausiids, appendicularians, and ostracods) had combined clearance rates of 2–81 L m-3 d-1 (mean of 19.6 L m-3 d-1). This implies a substantial impact on slowly sinking particles, but a negligible impact on the presumably rapidly-sinking fecal pellets that comprised the majority of the material collected in sediment traps. Our results highlight the need for a greater research focus on the many taxa that potentially act as flux feeders in the oceanic twilight zone.
Exosomes Derived From Septic Mouse Serum Modulate Immune Responses via Exosome-Associated Cytokines

Sepsis is a life-threatening condition caused by an immune response triggered by infection, and highly elevated cytokine/chemokine levels in the blood play crucial roles in the progression of sepsis. Serum exosomes are nanovesicles that have multiple biological functions, playing roles in antigen presentation, intercellular signal communication, inflammatory response and immune surveillance. However, the biological functions and related molecular bases remain to be elucidated. In this study, we investigated the profiles of cytokines/chemokines harbored in the exosomes of septic mice and explored the mechanisms of immunomodulation on T cells treated with exosomes harvested from septic mice. Blood cytokines/chemokines existed in both the soluble form and in the insoluble exosomal form; the profiles of the cytokines/chemokines in these two forms displayed different dynamics in the blood of mice challenged with LPS. Exosomes from septic mice induced the differentiation of Th1/Th2 cells, which was blocked by specific antibodies targeting IL-12 and IL-4. In addition, these exosomes significantly augmented the proliferation and migration of T lymphocytes. Furthermore, preadministration of exosomes by intravenous injection restrained the inflammatory response, attenuated lung and liver tissue damage, and prolonged the survival of cecal ligation and puncture (CLP) mice. Our results indicate that exosomes enriched with cytokines/chemokines play critical roles in T cell differentiation, proliferation and chemotaxis during the sepsis process and have a protective effect on cecal ligation and puncture (CLP) mice. Thus, these findings not only strengthen our understanding of the role of sepsis via exosomes but also provide potential targets for therapeutic applications.
Mesopelagic Sound Scattering Layers of the High Arctic: Seasonal Variations in Biomass, Species Assemblage, and Trophic Relationships

Mesopelagic sound scattering layers (SSL) are ubiquitous in all oceans. Pelagic organisms within the SSL play important roles as prey for higher trophic levels and in climate regulation through the biological carbon pump. Yet, the biomass and species composition of SSL in the Arctic Ocean remain poorly documented, particularly in winter. A multifrequency echosounder detected a SSL north of Svalbard, from 79.8°N to 81.4°N, in January 2016, August 2016, and January 2017. Midwater trawl sampling confirmed that the SSL comprised zooplankton and pelagic fish of boreal and Arctic origins. Juvenile beaked redfish dominated the fish assemblage in January and Arctic cod in August. The macrozooplankton community mainly comprised the medusa Cyanea capillata, the amphipod Themisto libellula, and the euphausiids Meganyctiphanes norvegica in August and Thysanoessa inermis in January. The SSL was located in the Atlantic Water mass, between 200-700 m in August and between 50-500 m in January. In January, the SSL was shallower and weaker above the deeper basin, where less Atlantic Water penetrated. The energy content available in the form of lipids within the SSL was significantly higher in summer than winter. The biomass within the SSL was >12-fold higher in summer, and the diversity of fish was slightly higher than in winter (12 vs. 9 species). We suggest that these differences are mainly related to life history and ontogenetic changes resulting in a descent towards the seafloor, outside the mesopelagic layer, in winter. In addition, some fish species of boreal origin, such as the spotted barracudina, did not seem to survive the polar night when advected from the Atlantic into the Arctic. Others, mainly juvenile beaked redfish, were abundant in both summer and winter, implying that the species can survive the polar night and possibly extend its range into the high Arctic. Fatty-acid trophic markers revealed that Arctic cod mainly fed on calanoid copepods while juvenile beaked redfish targeted krill (Thysanoessa spp.). The relatively high biomass of Arctic cod in August and of redfish in January thus suggests a shift within the SSL, from a Calanus-based food web in summer to a krill-based food web during winter.
Analysis of Self-Incompatibility and Genetic Diversity in Diploid and Hexaploid Plum Genotypes

During the last decade, S-genotyping has been extensively investigated in fruit tree crops such as those belonging to the Prunus genus, including plums. In plums, S-allele typing has been largely studied in diploid species but works are scarcer in polyploid species due to the complexity of the polyploid genome. This study was conducted in order to analyze the S-genotypes of 30 diploid P. salicina, 17 of them reported here for the first time, and 29 hexaploid plums (24 of P. domestica and 5 of P. insititia). PCR analysis allowed identifying nine S-alleles in the P. salicina samples allocating the 30 accessions in 16 incompatibility groups, two of them identified here for the first time. In addition, pollen tube growth was studied in self-pollinated flowers of 17 Tunisian P. salicina under the microscope. In 16 samples, including one carrying the Se allele, which has been correlated with self-compatibility, the pollen tubes were arrested in the style. Only in one cultivar (“Bedri”), the pollen tubes reached the base of the style. Twelve S-alleles were identified in the 24 P. domestica and 5 P. insititia accessions, assigning accessions in 16 S-genotypes. S-genotyping results were combined with nine SSR loci to analyze genetic diversity. Results showed a close genetic relationship between P. domestica and P. salicina and between P. domestica and P. insititia corroborating that S-locus genotyping is suitable for molecular fingerprinting in diploid and polyploid Prunus species.
Early Substance Use Cessation Improves Cognition—10 Years Outcome in First-Episode Psychosis Patients

Background: Cognitive impairment may be a risk factor for, as well as a consequence of, psychosis. Non-remitting symptoms, premorbid functioning, level of education, and socioeconomic background are known correlates. A possible confounder of these associations is substance use, which is common among patients with psychosis and linked to worse clinical outcomes. Studies however show mixed results for the effect of substance use on cognitive outcomes. In this study, the long-term associations of substance use with cognition in a representative sample of first-episode psychosis patients were examined. Methods: The sample consisted of 195 patients. They were assessed for symptom levels, function, and neurocognition at 1, 2, 5, and 10 years after first treatment. Test scores were grouped into factor analysis-based indices: motor speed, verbal learning, visuomotor processing, verbal fluency, and executive functioning. A standardized composite score of all tests was also used. Patients were divided into four groups based on substance-use patterns during the first 2 years of treatment: persistent users, episodic users, stop-users, and nonusers. Data were analyzed using linear mixed effects modeling. Results: Gender, premorbid academic functioning, and previous education were the strongest predictors of cognitive trajectories. However, on motor speed and verbal learning indices, patients who stopped using substances within the first 2 years of follow-up improved over time, whereas the other groups did not. For verbal fluency, the longitudinal course was parallel for all four groups, while patients who stopped using substances demonstrated superior performances compared with nonusers. Persistent users demonstrated impaired visuomotor processing speed compared with nonusers. Within the stop- and episodic use groups, patients with narrow schizophrenia diagnoses performed worse compared with patients with other diagnoses on verbal learning and on the overall composite neurocognitive index. Discussion: This study is one of very few long-term studies on cognitive impairments in first-episode psychosis focusing explicitly on substance use. Early cessation of substance use was associated with less cognitive impairment and some improvement over time on some cognitive measures, indicating a milder illness course and superior cognitive reserves to draw from in recovering from psychosis.
An Assessment of the Role of Women Group in Women Political Participation, and Economic Development in Nigeria

The exclusion of women in politics has been identified in recent times as one of the major setbacks for economic development. Women's groups are a strong pillar for grassroots politics; and a drive for more women participating in politics at the grassroots still faces a lot of challenges, making it difficult for them to harness available opportunities for economic development. Thus, the opportunity therein for more women's participation in politics and women empowerment is yet to be exploited by the women's groups in Nigeria. This present study assesses the role of women's groups in politics, identifies their challenges and also explores its implication for economic development in Osun state, Nigeria. The study was carried out using primary data from forums and dialogues within women's groups, consisting of an average of thirty (30) members from ten (10) local government areas (LGAs) in Osun state, Nigeria. In addition, explorative methods using existing literature were also employed. Findings from the study indicate that women's groups do not have political agenda; mostly, their goals do not align with any political agenda, although their members accept appointments, and also enjoy government patronage. There was also an indication that there exists a high illiteracy rate among the members of the women's groups and most of them are not aware of existing National or International gender equality laws or affirmative action. Thus, it is difficult to participate in politics and contribute their voices to political issues. The study concludes that the present role played by women's groups at the grassroots level may not be adequate in encouraging more women's participation in politics and in influencing economic development. Thus, there is need to step up their activities and embrace political issues if they are to help more women participate and be relevant in politics. The study therefore suggests that more empowerment programs, especially in the area of decision making and participation in politics, should be targeted at women's groups at the grassroots levels by the governments and all stakeholders as a matter of priority.
Collaborative intra-tumor heterogeneity detection

Abstract Motivation Despite the remarkable advances in sequencing and computational techniques, noise in the data and complexity of the underlying biological mechanisms render deconvolution of the phylogenetic relationships between cancer mutations difficult. Besides that, the majority of the existing datasets consist of bulk sequencing data of single tumor sample of an individual. Accurate inference of the phylogenetic order of mutations is particularly challenging in these cases and the existing methods are faced with several theoretical limitations. To overcome these limitations, new methods are required for integrating and harnessing the full potential of the existing data. Results We introduce a method called Hintra for intra-tumor heterogeneity detection. Hintra integrates sequencing data for a cohort of tumors and infers tumor phylogeny for each individual based on the evolutionary information shared between different tumors. Through an iterative process, Hintra learns the repeating evolutionary patterns and uses this information for resolving the phylogenetic ambiguities of individual tumors. The results of synthetic experiments show an improved performance compared to two state-of-the-art methods. The experimental results with a recent Breast Cancer dataset are consistent with the existing knowledge and provide potentially interesting findings. Availability and implementation The source code for Hintra is available at https://github.com/sahandk/HINTRA.
Volatile Flavor Components as a Function of Electrical Stimulation and Chiller Aging for m. longissimus and biceps femoris of Hanwoo Beef

Abstract The aim of the study was to evaluate the effect of an early post-mortem low voltage electrical stimulation (ES) to localized part of carcasses [m. longissimus lumborum (LL) and m. biceps femoris (BF)] and determined the tenderness and flavor compounds of Hanwoo steers (n=16). Carcasses were stimulated within 30 min post-mortem for 60s using 60 volts and muscles aged 2 and 14 d. Degradation of Troponin-T were accelerated by ES and degraded little faster in BF muscle than LL. Level of free amino acid content of stimulated and aged muscles was significantly (p<0.05) greater than control for both muscles. Totally 63 volatile compounds were identified by using SPME-GC. The ES treatment significantly (p<0.05) affected the level of 20 volatile compounds of LL as well 15 volatiles in BF muscle along with total amounts of ketones, sulfur containing, pyrazines and furans. Low voltage ES could be applied to reduce the aging time and improve volatile flavor development by increasing important desirable volatile compounds such as 2-methylpyrazine, 2,5-dimethylpyrazines and 2-acetylthiazole etc. due to released free amino acids from protein degradation.
Long-term efficacy and safety of paliperidone palmitate once-monthly in Chinese patients with recent-onset schizophrenia

Background: The subgroup analysis of a primary study (NCT01051531) evaluated the effect of long-term paliperidone palmitate once-monthly (PP1M) therapy in Chinese patients with recent-onset schizophrenia responding unsatisfactorily to previous oral antipsychotics. Patients and methods: This 18-month, open-label study consisted of 3 phases – screening (7 days), treatment (18 months) and end-of-study/withdrawal visit. All enrolled patients (18–50 years) received PP1M: 150 mg eq. (day 1), 100 mg eq. (day 8) followed by a once-monthly flexible dose (50, 75, 100 or 150 mg eq.). Efficacy and safety were assessed. Results: Among the 118 enrolled Chinese patients, 68 completed the treatment (mean age: 25.6 years; male: 54.7%). A clinically meaningful change from baseline to day 548 was observed in Positive and Negative Syndrome scale (primary endpoint, mean [SD]: −15.3 [20.76]), Personal and Social Performance scale (15.9 [19.65]), Clinician Global Impression-schizophrenia score (−1.2 [1.54]) and Medication Satisfaction Questionnaire score (0.9 [1.73]). Commonly reported treatment-emergent adverse events (TEAEs) included insomnia (13.9%), injection-site pain (13.9%), upper respiratory tract infection (13.0%), restlessness (13.0%) and akathisia (13.0%). Serious TEAEs were reported in 9.3% patients with schizophrenia being most common (6.5%) and one death (suicide) was observed. Conclusion: Efficacy of PP1M corroborate findings from earlier studies and no new safety concerns emerged in this Chinese subgroup of patients with schizophrenia.
A pooled meta-analysis of PD-1/L1 inhibitors incorporation therapy for advanced non-small cell lung cancer

Objective: Immune checkpoint inhibitors, especially the programmed cell death receptor-1/ligand 1 (PD-1/L1) inhibitors, displayed promising efficacy in non-small cell lung cancer (NSCLC) patients. Incorporation of anti-PD-1/L1 antibodies into other therapeutic regimens (including CTLA-4 inhibitors, chemotherapy, EGFR-TKIs and IDO inhibitors) is currently in active clinical research. This meta-analysis summarized recent developments in four combination regimens of PD-1/L1 inhibitors. Methods: We searched PubMed, the Cochrane Library and the Embase database up to July 2018, on the combination therapy of PD-1/L1 inhibitors in NSCLC patients. Results: Seventeen trials were finally included in the current meta-analysis. The combined objective response rate s (ORR) for PD-1/L1 inhibitors in combination with CTLA-4 inhibitors, chemotherapy, EGFR-TKIs, and IDO inhibitors were 32% (19%–44%), 49% (46%–53%), 55% (28%–83%) and 35% (20%–50%) respectively. The combined ORR for first line PD-1/L1 inhibitors combination with CTLA-4 inhibitors, chemotherapy, and EGFR-TKIs were 35% (17%–53%), 51% (46%–56%) and 43% (−7%–93%) respectively, and the combined ORR in the second or more line setting were 36% (8%–65%), 17% (−13%–46%), 39% (19%–59%) and 35% (20%–50%) respectively. The pooled 6-month progression-free survival rate (6m PFSr) and 1-year overall survival rate (1y OSr) for combination therapy of PD-1/L1 inhibitors with CTLA-4 inhibitors or chemotherapy were 35% or 65% (6m PFSr) and 31% or 70% (1y OSr) respectively. Anti-PD-1/L1 drugs combined with anti-CTLA-4 drugs exhibited a more potent efficacy on PD-L1 positive patients (OR=0.33, 95%CI: 0.12–0.88). This trend was not observed in patients receiving combination therapy of PD-1/L1 inhibitors with chemotherapy (OR=0.96, 95%CI: 0.51–1.78). Conclusion: The included four combination regimens were potential treatment strategies and well tolerated for NSCLC patients. Further, the therapy lines and PD-L1 expression status were correlated with treatment efficacy.
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm

Abstract Motivation Genome-wide identification of the transcriptomic responses of human cell lines to drug treatments is a challenging issue in medical and pharmaceutical research. However, drug-induced gene expression profiles are largely unknown and unobserved for all combinations of drugs and human cell lines, which is a serious obstacle in practical applications. Results Here, we developed a novel computational method to predict unknown parts of drug-induced gene expression profiles for various human cell lines and predict new drug therapeutic indications for a wide range of diseases. We proposed a tensor-train weighted optimization (TT-WOPT) algorithm to predict the potential values for unknown parts in tensor-structured gene expression data. Our results revealed that the proposed TT-WOPT algorithm can accurately reconstruct drug-induced gene expression data for a range of human cell lines in the Library of Integrated Network-based Cellular Signatures. The results also revealed that in comparison with the use of original gene expression profiles, the use of imputed gene expression profiles improved the accuracy of drug repositioning. We also performed a comprehensive prediction of drug indications for diseases with gene expression profiles, which suggested many potential drug indications that were not predicted by previous approaches. Supplementary information Supplementary data are available at Bioinformatics online.
Update on liquid biopsy in clinical management of non-small cell lung cancer

Abstract Lung cancer, a leading cause of cancer-related mortality, has a low rate of early diagnosis and a poor prognosis for advanced stages. Recent advances in further mastery of the biology of tumors promote the diagnosis and therapy, especially for non-small cell lung cancer (NSCLC). However, tumor tissue-based information is often not available in most cases due to the invasive and high risk nature of the tumor biopsy procedures. Liquid biopsy, based on the multiple liquid samples including circulating tumor cells (CTC), circulating tumor DNA (ctDNA), and tumor-derived exosome obtained from blood or urine as well as other body fluids, can also provide valuable tumor-related information, playing an important role in management of NSCLC in clinical practice. It is widely believed that concordance of detection for tumor by liquid samples in comparison with tissue biopsy for both early and advanced stage NSCLC patients is optimistic. We herein review the current and future clinical application of liquid biopsy, including early diagnosis and management of precise personalized treatment in lung cancer. The future directions of development for liquid biopsy are also discussed in this review.
PARP-1 inhibitor modulate β-catenin signaling to enhance cisplatin sensitivity in cancer cervix

Cisplatin is a keystone for treatment of both recurring and locally advanced cervical cancer. However toxic side effects and acquired resistance limits its efficacy. Enhanced DNA repair is one of the mechanisms through which cancer cells acquire cisplatin resistance. Inhibitors of PARP, which is a DNA damage repair enzyme, have been approved for use in BRCA mutated cancers like breast and ovary cancer. However little is known about the therapeutic efficacy of PARP inhibitors in cervical cancer, either as a single agent or in combination with cisplatin. We hypothesized that PARP-1 inhibition might improve the sensitivity of cervical cancer cells to cisplatin by diminishing DNA repair. To ascertain this, we determined effect of PARP-1 inhibition on cisplatin cytotoxicity in HeLa and SiHa cell lines. Combination of cisplatin with PJ34, a phenanthridinone-derived PARP-1 inhibitor, augmented cisplatin toxicity in vitro by decreasing cell proliferation, enhancing cell cycle block and cell death, and decreasing invasion and metastasis, when compared with either of the single agent alone. We further show that PARP-1 inhibition inhibited β-catenin signaling and its downstream components such as c-Myc, cyclin D1 and MMPs indicating a possible link between single strand base damage repair and WNT signaling. In conclusion, PARP-1 inhibition might augment cisplatin cytotoxicity in cervical cancer cells by modulating β-catenin signaling pathway. Combining PARP-1 inhibitors with cisplatin might be a promising approach to overcome cisplatin resistance and to achieve a better therapeutic effect.