Miracle-dz/UniFAR-FTUs huggingface dataset:
Augmenting Subarachnoid Block Analgesia in Caesarean Section Delivery with Sub-Psychotomimetic Dose of Ketamine

This study investigated the effect of low sub-psychotomimetic dose (0.3 mg/kg) of ketamine on subarachnoid block-induced analgesia with a view to assessing the analgesic effectiveness of combination of low dose ketamine with subarachnoid block in management of post caesarean section pain. Spinal anaesthesia was performed in 120 healthy pregnant women scheduled for elective caesarean delivery using 10 mg hyperbaric bupivacaine. Parturient mothers were randomly selected into four groups (n=30) consisting of K1, K2, NK1 and NK2. K1 received 0.3 mg/kg intravenous ketamine diluted with sterile water for injection to 5 mL, as a bolus dose 2 min before surgical incision; K2 was treated as K1 but at 2 minutes after delivery of baby, while NK1 and NK2 received equivalent volumes of normal saline 2 min before surgical incision and 2 min after baby extraction respectively. Age, weight, duration of surgery (DOS) and the time of first request for analgesia (TFA) for all participants were recorded. Post-operative pain intensity was assessed using a visual analogue scale (VASPI) at 2, 4, 8, 12, 24 and 36 h after spinal anaesthesia induction. Results were analyzed using ANOVA and Kruskal-Wallis tests. Student Newman-Keuls and Man-Whitney rank sum tests were used for post hoc analysis as appropriate. P value<0.05 was considered statistically significant. There was no significant difference in age and weight across groups, but duration of surgery was statistically prolonged in K1 group relative to NK1 group. Low dose ketamine significantly augmented the analgesic effect of spinal block anaesthesia, especially when given at two minutes before surgical incision.
A Predictive Coding Perspective on Beta Oscillations during Sentence-Level Language Comprehension

Oscillatory neural dynamics have been steadily receiving more attention as a robust and temporally precise signature of network activity related to language processing. We have recently proposed that oscillatory dynamics in the beta and gamma frequency ranges measured during sentence-level comprehension might be best explained from a predictive coding perspective. Under our proposal we related beta oscillations to both the maintenance/change of the neural network configuration responsible for the construction and representation of sentence-level meaning, and to top–down predictions about upcoming linguistic input based on that sentence-level meaning. Here we zoom in on these particular aspects of our proposal, and discuss both old and new supporting evidence. Finally, we present some preliminary magnetoencephalography data from an experiment comparing Dutch subject- and object-relative clauses that was specifically designed to test our predictive coding framework. Initial results support the first of the two suggested roles for beta oscillations in sentence-level language comprehension.
Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae

Extrachromosomal circular DNA (eccDNA) derived from chromosomal Ty retrotransposons in yeast can be generated in multiple ways. Ty eccDNA can arise from the circularization of extrachromosomal linear DNA during the transpositional life cycle of retrotransposons, or from circularization of genomic Ty DNA. Circularization may happen through nonhomologous end-joining (NHEJ) of long terminal repeats (LTRs) flanking Ty elements, by Ty autointegration, or by LTR–LTR recombination. By performing an in-depth investigation of sequence reads stemming from Ty eccDNAs obtained from populations of Saccharomyces cerevisiae S288c, we find that eccDNAs predominantly correspond to full-length Ty1 elements. Analyses of sequence junctions reveal no signs of NHEJ or autointegration events. We detect recombination junctions that are consistent with yeast Ty eccDNAs being generated through recombination events within the genome. This opens the possibility that retrotransposable elements could move around in the genome without an RNA intermediate directly through DNA circularization.
Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon

Oral iron administration in African children can increase the risk for infections. However, it remains unclear to what extent supplementary iron affects the intestinal microbiome. We here explored the impact of iron preparations on microbial growth and metabolism in the well-controlled TNO's in vitro model of the large intestine (TIM-2). The model was inoculated with a human microbiota, without supplementary iron, or with 50 or 250 μmol/L ferrous sulfate, 50 or 250 μmol/L ferric citrate, or 50 μmol/L hemin. High resolution responses of the microbiota were examined by 16S rDNA pyrosequencing, microarray analysis, and metagenomic sequencing. The metabolome was assessed by fatty acid quantification, gas chromatography-mass spectrometry (GC-MS), and 1H-NMR spectroscopy. Cultured intestinal epithelial Caco-2 cells were used to assess fecal water toxicity. Microbiome analysis showed, among others, that supplementary iron induced decreased levels of Bifidobacteriaceae and Lactobacillaceae, while it caused higher levels of Roseburia and Prevotella. Metagenomic analyses showed an enrichment of microbial motility-chemotaxis systems, while the metabolome markedly changed from a saccharolytic to a proteolytic profile in response to iron. Branched chain fatty acids and ammonia levels increased significantly, in particular with ferrous sulfate. Importantly, the metabolite-containing effluent from iron-rich conditions showed increased cytotoxicity to Caco-2 cells. Our explorations indicate that in the absence of host influences, iron induces a more hostile environment characterized by a reduction of microbes that are generally beneficial, and increased levels of bacterial metabolites that can impair the barrier function of a cultured intestinal epithelial monolayer.
Developmental Cognitive Neuroscience Neural Mirroring and Social Interaction: Motor System Involvement during Action Observation Relates to Early Peer Cooperation

Whether we hand over objects to someone, play a team sport, or make music together, social interaction often involves interpersonal action coordination, both during instances of cooperation and entrainment. Neural mirroring is thought to play a crucial role in processing other's actions and is therefore considered important for social interaction. Still, to date, it is unknown whether interindividual differences in neural mirroring play a role in interpersonal coordination during different instances of social interaction. A relation between neural mirroring and interpersonal coordination has particularly relevant implications for early childhood, since successful early interaction with peers is predictive of a more favorable social development. We examined the relation between neural mirroring and children's interpersonal coordination during peer interaction using EEG and longitudinal behavioral data. Results showed that 4-year-old children with higher levels of motor system involvement during action observation (as indicated by lower beta-power) were more successful in early peer cooperation. This is the first evidence for a relation between motor system involvement during action observation and interpersonal coordination during other instances of social interaction. The findings suggest that interindividual differences in neural mirroring are related to interpersonal coordination and thus successful social interaction.
Effect of Methotrexate on an In Vitro Patient-Derived Model of Proliferative Vitreoretinopathy

Purpose The purpose of this study was to develop a method for isolating, culturing, and characterizing cells from patient-derived membranes in proliferative vitreoretinopathy (PVR) to be used for drug testing. Methods PVR membranes were obtained from six patients with grade C PVR. Membrane fragments were analyzed by gross evaluation, fixed for immunohistologic studies to establish cell identity, or digested with collagenase II to obtain single cell suspensions for culture. PVR-derived primary cultures were used to examine the effects of methotrexate (MTX) on proliferation, migration, and cell death. Results Gross analysis of PVR membranes showed presence of pigmented cells, indicative of retinal pigment epithelial cells. Immunohistochemistry identified cells expressing α-smooth muscle actin, glial fibrillary acidic protein, Bestrophin-1, and F4/80, suggesting the presence of multiple cell types in PVR. Robust PVR primary cultures (C-PVR) were successfully obtained from human membranes, and these cells retained the expression of cell identity markers in culture. C-PVR cultures formed membranes and band-like structures in culture reminiscent of the human condition. MTX significantly reduced the proliferation and band formation of C-PVR, whereas it had no significant effect on cell migration. MTX also induced regulated cell death within C-PVR as assessed by increased expression of caspase-3/7. Conclusions PVR cells obtained from human membranes can be successfully isolated, cultured, and profiled in vitro. Using these primary cultures, we identified MTX as capable of significantly reducing growth and inducing cell death of PVR cells in vitro.
Experience with a second language affects the use of fundamental frequency in speech segmentation

This study investigates whether listeners’ experience with a second language learned later in life affects their use of fundamental frequency (F0) as a cue to word boundaries in the segmentation of an artificial language (AL), particularly when the cues to word boundaries conflict between the first language (L1) and second language (L2). F0 signals phrase-final (and thus word-final) boundaries in French but word-initial boundaries in English. Participants were functionally monolingual French listeners, functionally monolingual English listeners, bilingual L1-English L2-French listeners, and bilingual L1-French L2-English listeners. They completed the AL-segmentation task with F0 signaling word-final boundaries or without prosodic cues to word boundaries (monolingual groups only). After listening to the AL, participants completed a forced-choice word-identification task in which the foils were either non-words or part-words. The results show that the monolingual French listeners, but not the monolingual English listeners, performed better in the presence of F0 cues than in the absence of such cues. Moreover, bilingual status modulated listeners’ use of F0 cues to word-final boundaries, with bilingual French listeners performing less accurately than monolingual French listeners on both word types but with bilingual English listeners performing more accurately than monolingual English listeners on non-words. These findings not only confirm that speech segmentation is modulated by the L1, but also newly demonstrate that listeners’ experience with the L2 (French or English) affects their use of F0 cues in speech segmentation. This suggests that listeners’ use of prosodic cues to word boundaries is adaptive and non-selective, and can change as a function of language experience.
Bottom trawl fishing footprints on the world’s continental shelves

Significance We conducted a systematic, high-resolution analysis of bottom trawl fishing footprints for 24 regions on continental shelves and slopes of five continents and New Zealand. The proportion of seabed trawled varied >200-fold among regions (from 0.4 to 80.7% of area to a depth of 1,000 m). Within 18 regions, more than two-thirds of seabed area remained untrawled during study periods of 2–6 years. Relationships between metrics of total trawling activity and footprint were strong and positive, providing a method to estimate trawling footprints for regions where high-resolution data are not available. Trawling footprints were generally smaller in regions where fisheries met targets for exploitation rates, implying collateral environmental benefits of effective fisheries management. Bottom trawlers land around 19 million tons of fish and invertebrates annually, almost one-quarter of wild marine landings. The extent of bottom trawling footprint (seabed area trawled at least once in a specified region and time period) is often contested but poorly described. We quantify footprints using high-resolution satellite vessel monitoring system (VMS) and logbook data on 24 continental shelves and slopes to 1,000-m depth over at least 2 years. Trawling footprint varied markedly among regions: from <10% of seabed area in Australian and New Zealand waters, the Aleutian Islands, East Bering Sea, South Chile, and Gulf of Alaska to >50% in some European seas. Overall, 14% of the 7.8 million-km2 study area was trawled, and 86% was not trawled. Trawling activity was aggregated; the most intensively trawled areas accounting for 90% of activity comprised 77% of footprint on average. Regional swept area ratio (SAR; ratio of total swept area trawled annually to total area of region, a metric of trawling intensity) and footprint area were related, providing an approach to estimate regional trawling footprints when high-resolution spatial data are unavailable. If SAR was ≤0.1, as in 8 of 24 regions, there was >95% probability that >90% of seabed was not trawled. If SAR was 7.9, equal to the highest SAR recorded, there was >95% probability that >70% of seabed was trawled. Footprints were smaller and SAR was ≤0.25 in regions where fishing rates consistently met international sustainability benchmarks for fish stocks, implying collateral environmental benefits from sustainable fishing.
Modular 5′-UTR hexamers for context-independent tuning of protein expression in eukaryotes

Abstract Functional characterization of regulatory DNA elements in broad genetic contexts is a prerequisite for forward engineering of biological systems. Translation initiation site (TIS) sequences are attractive to use for regulating gene activity and metabolic pathway fluxes because the genetic changes are minimal. However, limited knowledge is available on tuning gene outputs by varying TISs in different genetic and environmental contexts. Here, we created TIS hexamer libraries in baker’s yeast Saccharomyces cerevisiae directly 5′ end of a reporter gene in various promoter contexts and measured gene activity distributions for each library. Next, selected TIS sequences, resulted in almost 10-fold changes in reporter outputs, were experimentally characterized in various environmental and genetic contexts in both yeast and mammalian cells. From our analyses, we observed strong linear correlations (R2 = 0.75–0.98) between all pairwise combinations of TIS order and gene activity. Finally, our analysis enabled the identification of a TIS with almost 50% stronger output than a commonly used TIS for protein expression in mammalian cells, and selected TISs were also used to tune gene activities in yeast at a metabolic branch point in order to prototype fitness and carotenoid production landscapes. Taken together, the characterized TISs support reliable context-independent forward engineering of translation initiation in eukaryotes.
Facilitating healthcare decisions by assessing the certainty in the evidence from preclinical animal studies

Laboratory animal studies are used in a wide range of human health related research areas, such as basic biomedical research, drug research, experimental surgery and environmental health. The results of these studies can be used to inform decisions regarding clinical research in humans, for example the decision to proceed to clinical trials. If the research question relates to potential harms with no expectation of benefit (e.g., toxicology), studies in experimental animals may provide the only relevant or controlled data and directly inform clinical management decisions. Systematic reviews and meta-analyses are important tools to provide robust and informative evidence summaries of these animal studies. Rating how certain we are about the evidence could provide important information about the translational probability of findings in experimental animal studies to clinical practice and probably improve it. Evidence summaries and certainty in the evidence ratings could also be used (1) to support selection of interventions with best therapeutic potential to be tested in clinical trials, (2) to justify a regulatory decision limiting human exposure (to drug or toxin), or to (3) support decisions on the utility of further animal experiments. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) approach is the most widely used framework to rate the certainty in the evidence and strength of health care recommendations. Here we present how the GRADE approach could be used to rate the certainty in the evidence of preclinical animal studies in the context of therapeutic interventions. We also discuss the methodological challenges that we identified, and for which further work is needed. Examples are defining the importance of consistency within and across animal species and using GRADE’s indirectness domain as a tool to predict translation from animal models to humans.
Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction – and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology‐guided metabolic engineering offers to tackle these issues.
MATI: An efficient algorithm for influence maximization in social networks

Influence maximization has attracted a lot of attention due to its numerous applications, including diffusion of social movements, the spread of news, viral marketing and outbreak of diseases. The objective is to discover a group of users that are able to maximize the spread of influence across a network. The greedy algorithm gives a solution to the Influence Maximization problem while having a good approximation ratio. Nevertheless it does not scale well for large scale datasets. In this paper, we propose Matrix Influence, MATI, an efficient algorithm that can be used under both the Linear Threshold and Independent Cascade diffusion models. MATI is based on the precalculation of the influence by taking advantage of the simple paths in the node’s neighborhood. An extensive empirical analysis has been performed on multiple real-world datasets showing that MATI has competitive performance when compared to other well-known algorithms with regards to running time and expected influence spread.
The Preferred Retinal Locus Used to Watch Videos

Purpose Eccentric viewing is a common strategy used by people with central vision loss (CVL) to direct the eye such that the image falls onto functioning peripheral retina, known as the preferred retinal locus (PRL). It has been long acknowledged that we do not know whether the PRL used in a fixation test is also used when performing tasks. We present an innovative method to determine whether the same PRL observed during a fixation task was used to watch videos and whether poor resolution affects gaze location. Methods The gaze of a group of 60 normal vision (NV) observers was used to define a democratic center of interest (COI) of video clips from movies and television. For each CVL participant (N = 20), we computed the gaze offsets from the COI across the video clips. The distribution of gaze offsets of the NV participants was used to define the limits of NV behavior. If the gaze offset was within this 95% degree confidence interval, we presumed that the same PRL was used for fixation and video watching. Another 15 NV participants watched the video clips with various levels of defocus blur. Results CVL participants had wider gaze-offset distributions than NV participants (P < 0.001). Gaze offsets of 18/20 CVL participants were outside the NV confidence interval. Further, none of the 15 NV participants watching the same videos with spherical defocus blur had a gaze offset that was decentered (outside the NV confidence interval), suggesting that resolution was not the problem. Conclusions This indicates that many CVL participants were using a PRL to view videos that differed from that found with a fixation task and that it was not caused by poor resolution alone. The relationship between these locations needs further investigation.
Clinical Implications of Co-Inhibitory Molecule Expression in the Tumor Microenvironment for DC Vaccination: A Game of Stop and Go

The aim of therapeutic dendritic cell (DC) vaccines in cancer immunotherapy is to activate cytotoxic T cells to recognize and attack the tumor. T cell activation requires the interaction of the T cell receptor with a cognate major-histocompatibility complex-peptide complex. Although initiated by antigen engagement, it is the complex balance between co-stimulatory and co-inhibitory signals on DCs that results in T cell activation or tolerance. Even when already activated, tumor-specific T cells can be neutralized by the expression of co-inhibitory molecules on tumor cells. These and other immunosuppressive cues in the tumor microenvironment are major factors currently hampering the application of DC vaccination. In this review, we discuss recent data regarding the essential and complex role of co-inhibitory molecules in regulating the immune response within the tumor microenvironment. In particular, possible therapeutic intervention strategies aimed at reversing or neutralizing suppressive networks within the tumor microenvironment will be emphasized. Importantly, blocking co-inhibitory molecule signaling, often referred to as immune checkpoint blockade, does not necessarily lead to an effective activation of tumor-specific T cells. Therefore, combination of checkpoint blockade with other immune potentiating therapeutic strategies, such as DC vaccination, might serve as a synergistic combination, capable of reversing effector T cells immunosuppression while at the same time increasing the efficacy of T cell-mediated immunotherapies. This will ultimately result in long-term anti-tumor immunity.