Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistence of Suspected Probiotic Organisms in Preterm Infant Gut Microbiota Weeks After Probiotic Supplementation in the NICU

Probiotics are becoming a prevalent supplement to prevent necrotizing enterocolitis in infants born preterm. However, little is known about the ability of these live bacterial supplements to colonize the gut or how they affect endogenous bacterial strains and the overall gut community. We capitalized on a natural experiment resulting from a policy change that introduced the use of probiotics to preterm infants in a single Neonatal Intensive Care Unit. We used amplicon sequence variants (ASVs) derived from the v3 region of the 16S rRNA gene to compare the prevalence and abundance of Bifidobacterium and Lactobacillus in the gut of preterm infants who were and were not exposed to a probiotic supplement in-hospital. Infants were followed to 5 months corrected age. In the probiotic-exposed infants, ASVs belonging to species of Bifidobacterium appeared at high relative abundance during probiotic supplementation and persisted for up to 5 months. In regression models that controlled for the confounding effects of age and antibiotic exposure, probiotic-exposed infants had a higher abundance of the suspected probiotic bifidobacteria than unexposed infants. Conversely, the relative abundance of Lactobacillus was similar between preterm groups over time. Lactobacillus abundance was inversely related to antibiotic exposure. Furthermore, the overall gut microbial community of the probiotic-exposed preterm infants at term corrected age clustered more closely to samples collected from 10-day old full-term infants than to samples from unexposed preterm infants at term age. In conclusion, routine in-hospital administration of probiotics to preterm infants resulted in the potential for colonization of the gut with probiotic organisms post-discharge and effects on the gut microbiome as a whole. Further research is needed to fully discriminate probiotic bacterial strains from endogenous strains and to explore their functional role in the gut microbiome and in infant health.
Microbes Help Predict More Efficient Cattle

The number of people in the world is rapidly growing and with more people comes the need for more food. Luckily, cattle are a great resource to help provide more food! These animals can produce more protein than they consume, converting human-inedible grasses into high-quality protein for humans to eat. However, we can still improve this conversion of grasses to meat by making cattle more efficient at the process, otherwise known as making cattle more feed efficient. In this study, we identified stomach microbes and blood nutrients of feed-efficient cattle. Using computers, we were able to show that the nutrients in the blood could predict the microbes living in the stomachs of feed-efficient cattle. This work shows that microbes in the stomachs of cattle may help improve feed efficiency and can be used to predict which cattle are feed efficient.
Mesenchymal Stromal Cells as Critical Contributors to Tissue Regeneration

Adult stem cells that are tightly regulated by the specific microenvironment, or the stem cell niche, function to maintain tissue homeostasis and regeneration after damage. This demands the existence of specific niche components that can preserve the stem cell pool in injured tissues and restore the microenvironment for their subsequent appropriate functioning. This role may belong to mesenchymal stromal cells (MSCs) due to their resistance to damage signals and potency to be specifically activated in response to tissue injury and promote regeneration by different mechanisms. Increased amount of data indicate that activated MSCs are able to produce factors such as extracellular matrix components, growth factors, extracellular vesicles and organelles, which transiently substitute the regulatory signals from missing niche cells and restrict the injury-induced responses of them. MSCs may recruit functional cells into a niche or differentiate into missing cell components to endow a niche with ability to regulate stem cell fates. They may also promote the dedifferentiation of committed cells to re-establish a pool of functional stem cells after injury. Accumulated evidence indicates the therapeutic promise of MSCs for stimulating tissue regeneration, but the benefits of administered MSCs demonstrated in many injury models are less than expected in clinical studies. This emphasizes the importance of considering the mechanisms of endogenous MSC functioning for the development of effective approaches to their pharmacological activation or mimicking their effects. To achieve this goal, we integrate the current ideas on the contribution of MSCs in restoring the stem cell niches after damage and thereby tissue regeneration.
Predicting Thermal Adaptation by Looking Into Populations’ Genomic Past

Molecular evolution offers an insightful theory to interpret the genomic consequences of thermal adaptation to previous events of climate change beyond range shifts. However, disentangling often mixed footprints of selective and demographic processes from those due to lineage sorting, recombination rate variation, and genomic constrains is not trivial. Therefore, here we condense current and historical population genomic tools to study thermal adaptation and outline key developments (genomic prediction, machine learning) that might assist their utilization for improving forecasts of populations’ responses to thermal variation. We start by summarizing how recent thermal-driven selective and demographic responses can be inferred by coalescent methods and in turn how quantitative genetic theory offers suitable multi-trait predictions over a few generations via the breeder’s equation. We later assume that enough generations have passed as to display genomic signatures of divergent selection to thermal variation and describe how these footprints can be reconstructed using genome-wide association and selection scans or, alternatively, may be used for forward prediction over multiple generations under an infinitesimal genomic prediction model. Finally, we move deeper in time to comprehend the genomic consequences of thermal shifts at an evolutionary time scale by relying on phylogeographic approaches that allow for reticulate evolution and ecological parapatric speciation, and end by envisioning the potential of modern machine learning techniques to better inform long-term predictions. We conclude that foreseeing future thermal adaptive responses requires bridging the multiple spatial scales of historical and predictive environmental change research under modern cohesive approaches such as genomic prediction and machine learning frameworks.
Communicating Science With YouTube Videos: How Nine Factors Relate to and Affect Video Views

Recent works about science communication through online videos on YouTube have focused mostly on categorization, content description, and the video's approach to scientific themes. However, still little is known about factors affecting science video popularity on the platform. This study aims to describe the relationship between nine content-related and content-agnostic factors, and the popularity of science videos on YouTube, defined as the number of views per days since the video posting. We collected a sample of 441 semi-randomly selected videos produced by the ScienceVlogs Brasil project – a Brazilian alliance of science channels hosted by independent science communicators on YouTube. Content-related factors were video theme, video format and video editing features, while content-agnostic factors were video length, video age, channel productivity, number of likes, number of comments and channel to which the video belongs. Descriptive and inferential analyses were performed with the R software to assess the correlation of each factor with the popularity of each video. Descriptive results show that the most popular science videos are those with interdisciplinary themes, styled either as vlog, animation or group conversation, and those belonging to the channels “Ciência Todo Dia,” “Minuto da Terra,” “Canal do Pirula” e “Papo de Biólogo. ” The inferential analysis shows that the most relevant factors to predict popularity, according to our model, are number of likes per video, channel productivity, video age and video format.
Development of a Method for Simultaneous Generation of Multiple Genetic Modification in Salmonella enterica Serovar Typhimurium

To comprehensively analyze bacterial gene function, it is important to simultaneously generate multiple genetic modifications within the target gene. However, current genetic engineering approaches, which mainly use suicide vector- or λ red homologous recombination-based systems, are tedious and technically difficult to perform. Here, we developed a flexible and easy method to simultaneously construct multiple modifications at the same locus on the Salmonella enterica serovar Typhimurium chromosome. The method combines an efficient seamless assembly system in vitro, red homologous recombination in vivo, and counterselection marker sacB. To test this method, with the seamless assembly system, various modification fragments for target genes cpxR, cpxA, and acrB were rapidly and efficiently constructed in vitro. sacBKan cassettes generated via polymerase chain reaction were inserted into the target loci in the genome of Salmonella Typhimurium strain CVCC541. The resulting pKD46-containing kanamycin-resistant recombinants were selected and used as intermediate strains. Multiple target gene modifications were then carried out simultaneously via allelic exchange using various homologous recombinogenic DNA fragments to replace the sacBKan cassettes in the chromosomes of the intermediate strains. Using this method, we successfully carried out site-directed mutagenesis, seamless deletion, and 3 × FLAG tagging of the target genes. This method can be used in any bacterial species that supports sacB gene activity and λ red-mediated recombination, allowing in-depth functional analysis of bacterial genes.
Eta-Equivalence in Core Dependent Haskell

We extend the core semantics for Dependent Haskell with rules for η -equivalence. This semantics is deﬁned by two related calculi, Systems D and DC. The ﬁrst is a Curry-style dependently-typed language with nontermination, irrelevant arguments, and equality abstraction. The second, inspired by the Glasgow Haskell Compiler’s core language FC, is the explicitly-typed analogue of System D, suitable for implementation in GHC. Our work builds on and extends the existing metatheory for these systems developed using the Coq proof assistant
Bank Competition in Africa: Do Institutional Quality and Cross-border Banking Matter?

ABSTRACT This paper analyses the implications of cross-border banking (CBB) and institutional quality (IQ) for bank competition in Africa. It applies a two-step estimation procedure using bank-level panel data for 29 African countries. In step one, the Boone indicator and the Lerner index are used to gauge bank competition in a given country in Africa. In the second step, it analyzes the sources of bank competition placing emphasis on the impact of CBB and IQ. The results suggest that competition increased in the period of 2002–2005, before decreasing somewhat between 2006 and 2007 and increasing again thereafter. The results also show that cross-border banking enhances bank competition in African countries with stronger governance structures and institutional quality. These results are robust to an array of controls including an alternative methodology, variable specifications, and the regulatory environments that banks operate in.
Big Step Normalisation for Type Theory

Big step normalisation is a normalisation method for typed lambda-calculi which relies on a purely syntactic recursive evaluator. Termination of that evaluator is proven using a predicate called strong computability, similar to the techniques used to prove strong normalisation of β -reduction for typed lambda-calculi. We generalise big step normalisation to a minimalist dependent type theory. Compared to previous presentations of big step normalisation for e.g. the simply-typed lambda-calculus, we use a quotiented syntax of type theory, which crucially reduces the syntactic complexity introduced by dependent types. Most of the proof has been formalised using Agda. 2012
Long‐chain n‐3 fatty acids – New anabolic compounds improving protein metabolism

Previous animal studies demonstrated that chronic feeding of long‐chain n‐3 polyunsaturated fatty acids (LCn‐3PUFA) that modifies muscle membrane fatty acid composition promotes protein anabolism by blunting the age‐associated deterioration in insulin sensitivity. The current study assessed, as a proof of concept, the anabolic effects of LCn‐3PUFA‐rich menhaden oil in 78 male castrated pigs (20 kg initial body weight). Pigs were fed for 76 days diets containing 0, 3, or 4% menhaden oil using iso‐energetic oil substitutions in diets typical of swine production (6% fat matter). Performance and body composition were measured using ultrasound technology during growth at 55 and 85 kg according to a complete block design. Menhaden oil feeding linearly reduced feed intake with a decline from 2.58 to 2.51 kg/d (‐3%; P=0.04) at 85 kg body weight without altering body weight gain. Back fat thickness remained unchanged (11.16 mm) between treatments. The diameter of the longissimus dorsi was linearly increased as menhaden oil amount increased (50.0, 50.1, 51.8 mm; P=0.02). The results demonstrate for the first time that LCn‐3PUFA promote muscle protein accretion, this approach could be a novel intervention to ameliorate the age‐related loss of muscle mass in the human.
ASSESSMENT OF THE INSECTICIDAL POTENCY OF NEEM (Azadirachta indica) SEED KERNEL METHANOLIC AND AQUEOUS EXTRACTS ON THE MALARIA VECTOR Anopheles gambiae

The potency of aqueous and methanolic extracts of neem (Azadirachta indica A. Juss) seed kernel, in inhibiting and disrupting development of Anopheles mosquito was assessed in the laboratory. Different concentrations of aqueous and methanolic extracts were tested on eggs, larvae and pupae. Both extracts were found to cause mortality on the specimens used and the level of mortality was concentration dependent. Mortality increased as the concentration increased. Methanolic extract of the neem seed kernel caused significantly higher (P = 0.05) mortality than aqueous extract. Few adults emerged among those treated with lowest concentration of 1 %( wt./vol.) aqueous extract, whereas no larvae or pupae survived to next stage in methanolic extract of the same concentrations. At highest concentration of 5 % (wt/vol), both extracts caused 100% mortality of larvae although the methanolic extract gave a quicker kill (12 hours) than the aqueous extract (24 hours). No egg hatched in all concentrations of both extracts.
Biochemical and Serological Characteristics, Drug Resistance and Plasmid Profiles of Spanish Isolates of Aeromonas salmonicida

We conducted a comparative study of Aeromonas salmonicida strains isolated in the Northwest of Spain from salmon and trout (Oncorhynchus mykiss, Salmo salar and S. trutta) cultured in fresh and sea waters with reference strains from different countries. Regardless of the geographic origin and source of isolation, all strains were biochemically and serolo gically similar, belonging to A. salmonicida subsp. salmonicida. All the isolates exhibited a uniform plasmid pattern. The majority of them (93%) carried three small plasmids of 3.6, 3.5 and 3.4 Megadaltons (Md). In addition, a fourth plasmid of 4.2 Md was present in 21 of the 32 strains examined. Only in some isolates a large plasmid was detected in the range of 40-55 Md. A high number of the Spanish isolates were resistant to oxolinic acid and flumequine. However no correlation between plasmid content and drug resistances was observed. The phenotypic and genetic homogeneity of the pigmented A. salmonicida strains make very difficult the determination of the origin of furunculosis in a particular geogra phic area.
Proteolytic activity in Caenorhabditis elegans : soluble and insoluble fractions

Proteolytic activities of soluble and insoluble fractions of the free-living soil nematode Caenorhabditis elegans were measured across a range of substrates, temperatures and pH conditions. Several protease inhibitors were also tested under these conditions. Results of these studies indicate that proteolytic activity is present in cytosolic (CF) and non-cytosolic (NCF) fractions of C. elegans extracts at every condition of pH, temperature and buffer assayed. On the other hand, the use of different protease inhibitors demonstrated the existence of exo and endoproteases types in CF as well as NCF. Moreover our results show that the use of two protease inhibitor mixed types proposed by several authors are not enough to avoid this lytic activity when homogenates of this nematode are employed in biochemical assays.
The Impacts of DNS Protocol Security Weaknesses

Global DNS infrastructure is a major component for the services exposed in the internet. The purpose of the study is understanding the cyber security status of DNS ecosystem. As part of the research, a statistical analysis based on vulnerability repositories has been created to provide a view toward the level of DNS security in general. It can help organizations to understand, assess and mitigate DNS risks. It's made short review of most used attacks against DNS and mitigation: amplification, reflection, floods, DNS exploits, and analysis for the DNS security incidents trend. The statistics implicitly reflect the degree of adoption of new DNS security standards and technologies.
Effects of Antibiotics on the Dynamic Balance of Bacteria and Fungi in the Gut of the German Cockroach

Abstract The German cockroach, Blattella germanica (L.) (Blattaria: Blattidae) harbored diverse microorganisms in the digestive tract, including bacteria, fungi, viruses, archaea, and protozoa. This diverse community maintains a relatively stable balance. Some bacteria have been confirmed to play crucial roles in the insect's physiology, biochemistry, and behavior. Antibiotics can effectively eliminate bacteria and disrupt the balance of gut microbiota, but the time-course of this process, the structure of the new microbial community, and the dynamics of re-assemblage of a bacterial community after antibiotic treatment have not been investigated. In the present study, antibiotic (levofloxacin and gentamicin) ingestion reduced bacterial diversity and abundance in the cockroach gut. Within 14 d of discontinuing antibiotic treatment, the number of culturable gut bacteria returned to its original level. However, the composition of the new bacterial community with greater abundance of antibiotic-resistant Enterococcus and Dysgonomonas was significantly different from the original community. Network analysis showed that antibiotic treatment made the interaction between bacteria and fungi closer and stronger in the cockroach gut during the recovery of gut microorganisms. The study on the composition change, recovery rules, and interaction dynamics between gut bacteria and fungi after antibiotic treatment are helpful to explore gut microbes' colonization and interaction with insects, which contributes to the selection of stable core gut bacteria as biological carriers of paratransgenesis for controlling Blattella germanica.
A minimal physiologically based pharmacokinetic model to characterize colon TNF suppression and treatment effects of an anti-TNF monoclonal antibody in a mouse inflammatory bowel disease model

ABSTRACT Biotherapeutic drugs against tumor necrosis factor (TNF) are effective treatments for moderate to severe inflammatory bowel disease (IBD). Here, we evaluated CNTO 5048, an antimurine TNF surrogate monoclonal antibody (mAb), in a CD45RBhigh adoptive T cell transfer mouse colitis model, which allows examination of the early immunological events associated with gut inflammation and the therapeutic effects. The study was designed to quantitatively understand the effects of IBD on CNTO 5048 disposition, the ability of CNTO 5048 to neutralize pathogenic TNF at the colon under disease conditions, and the impact of dosing regimen on CNTO 5048 treatment effect. CNTO 5048 and TNF concentrations in both mice serum and colon homogenate were also measured. Free TNF concentrations in colon, but not in serum, were shown to correlate well with the colon pharmacodynamic readout, such as the summed histopathology score and neutrophil score. A minimal physiologically based pharmacokinetic (mPBPK) model was developed to characterize CNTO 5048 PK and disposition, as well as colon soluble TNF target engagement (TE). The mPBPK/TE model reasonably captured the observed data and provided a quantitative understanding of an anti-TNF mAb on its colon TNF suppression and therapeutic effect in a physiologically relevant IBD animal model. These results also provided insights into the potential benefits of using induction doses for the treatment of IBD patients.
Animal navigation: a noisy magnetic sense?

ABSTRACT Diverse organisms use Earth's magnetic field as a cue in orientation and navigation. Nevertheless, eliciting magnetic orientation responses reliably, either in laboratory or natural settings, is often difficult. Many species appear to preferentially exploit non-magnetic cues if they are available, suggesting that the magnetic sense often serves as a redundant or ‘backup’ source of information. This raises an interesting paradox: Earth's magnetic field appears to be more pervasive and reliable than almost any other navigational cue. Why then do animals not rely almost exclusively on the geomagnetic field, while ignoring or downplaying other cues? Here, we explore a possible explanation: that the magnetic sense of animals is ‘noisy’, in that the magnetic signal is small relative to thermal and receptor noise. Magnetic receptors are thus unable to instantaneously acquire magnetic information that is highly precise or accurate. We speculate that extensive time-averaging and/or other higher-order neural processing of magnetic information is required, rendering the magnetic sense inefficient relative to alternative cues that can be detected faster and with less effort. This interpretation is consistent with experimental results suggesting a long time course for magnetic compass and map responses in some animals. Despite possible limitations, magnetoreception may be maintained by natural selection because the geomagnetic field is sometimes the only source of directional and/or positional information available. Summary: Magnetic orientation responses in animals are often weak and difficult to elicit experimentally. A possible explanation is that the magnetic compass is ‘noisy’ and cannot acquire precise magnetic information over short time periods.
EFEITOS BACTERIOSTÁTICOS E BACTERICIDA DE ANTIBIÓTICOS SOBRE AS LISTERIA spp ISOLADAS EM GOIÂNIA DE PACIENTES COM CLÍNICA DE ABORTO REPETITIVO

Neste estudo foi verificado a susceptibilidade "in vilro" aos anlimicrobianos de Listeria sppisolados de endocervix de mulheres com clinica de aborto repetitivo. O tratamento de listeriose comantibioticos mais frequentemente recomendados (penicilina e ampicilina) sao geralmente bem sucedidos.porem ha varios casos notificados de falhas terapeuticas. Foi utilizado o metodo de macrodiluicao em tubopara determinar as concentracoes minimas inibitorias (MICs) e as concentracoes minimas bactericidas(MBCs). A ampicilina e a penicilina foram bacteriostaticas para as Listeria spp. A gemamicina e aciprofloxacina foram bactericidas onde MBCs foram ate 3 vezes maiores que as respectivas CMIs. Poroutro lado as CMBs de penicilina e ampicilina foram pelo menos 6 vezes maiores que CMIs. Tresamostras de Listeria monocytogcnes mostraram tolerância para com penicilina e ampicilina.