Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and application of graph-based computational methods to elucidate the functional role of metabolism in human skin

1 Abstract The epidermis is the outermost layer of human skin and constitutes the first barrier to prevent body water loss and protect inner tissue against environmental cues like microbes, physical injury or ultraviolet radiation. This barrier function is maintained through the continuous renewal of the epidermis by proliferating and differentiating keratinocyte stem cells in a process called epidermal homeostasis. Importantly, disturbances of the proliferationdifferentiation balance of keratinocytes can induce a disrupted epidermal barrier and cause severe skin diseases such as psoriasis or cancer. The energy and molecular precursors necessary to maintain cellular functions in living organisms are provided by metabolism. In recent years, it became evident that a strong crosstalk exists between metabolism and the cellular signaling processes determining cellular fate including proliferation-differentiation transition of stem cells. In humans, individual cues indicated that metabolism is involved in sustaining and maintaining important skin functions such as epidermal homeostasis. However, to date there is no complete understanding of the detailed metabolic rewiring involved in epidermal homeostasis, maintenance of the epidermal barrier, and protection of keratinocytes against environmental stressors. The notion that metabolism is involved in important crosstalk with diverse signaling processes supported by technological advances in analytical methods motivated a variety of discovery-driven, large-scale metabolomics studies in fields reaching from biotechnology to human health and disease. Despite the increased availability of large metabolomics datasets, researches often have to rely on simple statistics for data analysis, although the myriad of interconversions between metabolites make manual data interpretation barely feasible. Thus, to date one of the major bottlenecks in the field of metabolomics is the lack of sophisticated metabolic-network driven computational approaches that facilitate data interpretation. In this thesis, we tackle shortcomings both in the interpretation of large-scale metabolomics data (chapters 4 to 6) and in the understanding of the functional role of metabolism in human skin within three processes: epidermal homeostasis (chapter 3 and 6), oxidative stress response (chapter 7) and skin aging (chapter 8). To set the stage for this work, we review recent achievements of targeted and non-targeted metabolomics studies in chapter 2 and compare their contribution on generating novel biological insights in the fields of bacterial communication, biotechnology, functional genomics as well as human health and disease. We conclude that non-targeted metabolomics studies rarely provided mechanistic insights and argue that further advanced
Biology and external morphology of invasive tomato leaf miner, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae)

The tomato leaf miner, Tuta absoluta (Meyrick), native to South America, has gained entry to India in the recent past. Being an exotic pest, generating information on biology under local conditions is essential. The incubation, larval and pupal periods were 3.90±0.91, 11.80±1.25 and 9.15±1.70 days, respectively. There were four larval instars based on head capsule collected. Characters useful to distinguish sex in different stages like larvae, pupa and adults were identified. Larvae were sexed based on the presence of pink coloured gonads in males, pupae based on the distance of genital aperture from the anterior segment of last segment and adults based on the abdominal size and genitalia. Description of male and female genitalia has been given. The study is helpful in designing future integrated management of this recently invaded pest in India.
Phylogenetic relationships of Pieridae (Lepidoptera: Papilionoidea) in China based on seven gene fragments

The butterfly family Pieridae includes approximately 1000 described extant species distributed worldwide. Among these, 154 species belonging to 24 genera are recorded in China. There has been no previous comprehensive phylogenetic study of the molecular phylogeny of Chinese pierids based on molecular data. In this study, 52 species representing 21 genera distributed in China were sampled. We reconstructed their evolutionary history based on four mitochondrial (COII, ND1, Cytb and 16S rDNA) and three nuclear (28S rRNA (D2–D3), 28S rRNA (D8) and EF‐1α) gene fragments using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI). Our results are congruent with recent studies and support the monophyly of three subfamilies, with Dismorphiinae sister to Coliadinae + Pierinae. Relationships among five genera of Coliadinae are: Eurema + (Dercas + (Goneperyx + (Catopsilia + Colias))). Relationships among the largest subfamily Pierinae are consistently recovered as follows: Leptosiaini + ((Nepheroniini + Teracolini) + (Anthocharidini + Pierini)). The division of three subgenera of Aporia (Aporia, Metaporia and Mesapia) is not supported because both the Aporia (Aporia) and Aporia (Metaporia) are found to be strongly paraphyletic, with Mesapia nested within Aporia sensu lato.
Sexual Dimorphism and Allometric Growth in the Enigmatic Pygmy Crab Petramithrax Pygmaeus (Bell, 1836) (Decapoda: Brachyura: Mithracidae), with a Formal Test of Rensch’s Rule in Spider Crabs (Superfamily Majoidea)

Rensch’s rule, a well-studied macroevolutionary pattern of sexual size dimorphism (SSD), predicts, in monophyletic taxa in which males are the larger sex, that as the body size of the species in the clade increases, SSD increases as well. We tested Rensch’s rule in the superfamily Majoidea, a diverse clade of ‘spider crabs. ’ Considering that having the widest range of data available is important when testing macroevolutionary hypotheses, we first explored SSD in the pygmy spider crab Petramithrax pygmaeus (Bell, 1836), one of the smallest spider crabs in the superfamily. Petramithrax pygmaeus exhibits an unusual pattern of sexual dimorphism, with females displaying a larger average carapace width than males, yet males attain a larger overall body size. This type of SSD is unusual for spider crabs, with most species displaying male-biased sexual size dimorphism for both mean and overall body size. Hierarchical cluster and discriminant analyses demonstrated the existence of two distinct ontogenetic phases in P. pygmaeus (juvenile/prepubertal and adult/postpubertal). We used our data on body size of P. pygmaeus along with previously published body-size data for 11 other species within the superfamily Majoidea to test for Rensch’s rule. Using raw data, phylogenetic independent contrasts generated from maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees, and reduced major axis regression analyses, we determined that for the tested species in the Majoidea that the predictions of Rensch’s rule were not upheld. Macroevoultionary patterns such as Rensch’s rule are not well studied in marine invertebrate systems; looking at how these rules compare between vertebrate and invertebrate and terrestrial and aquatic animals will help us to understand the differences and factors that could influence size and growth in these systems.
Prevalence of Listeria in Smoked Fish.

Smoked fish samples (71) were surveyed from Newfoundland retail markets and tested for the prevalence of Listeria . Staphylococcus aureus and fecal coliforms were also detected in the samples. Listeria was present in 11.3% of the smoked seafood products; 4 smoked cod, 3 smoked mackerel, and 1 smoked caplin were found to harbor the bacterium. The Food and Drug Administration protocol was also analyzed with regards to testing smoked seafoods. The secondary enrichment broth showed a 68% false-positive rate, whereas all positive samples were detected after 24 h of primary enrichment.
Male genital ducts in the salamanders Eurycea lucifuga and Eurycea longicauda

The excurrent ducts of the reproductive system of male salamanders show great variation among species of several families, with those of two species of Eurycea being the simplest yet described. Each testis of E. longicauda and E. lucifuga is drained by 5-6 equally spaced transverse tubules passing directly from the central testicular duct to the vas deferens. There is no longitudinal collecting duct between the testis and vas deferens, and no histological regionalization of the transverse tubules nor vasa deferentia. Renal corpuscles, present in at least a reduced condition in the epididymal nephrons of other species, are not present in either species of Eurycea. Histological and histochemical features of the ducts of both species reflect seasonal activity. THE sperm transport system of sala- manders consists of a series of excurrent ducts carrying spermatozoa from the tes- tis, through the epididymal portion of the kidney, to the cloaca. These ducts also store spermatozoa prior to mating. During a preliminary investigation of the male re- productive system of the cave salaman-
Systematic review of reviews of symptoms and signs of COVID-19 in children and adolescents

Objective To undertake a systematic review of reviews of the prevalence of symptoms and signs of COVID-19 in those aged under 20 years. Design Narrative systematic review of reviews. PubMed, medRxiv, Europe PMC and COVID-19 Living Evidence Database were searched on 9 October 2020. Setting All settings, including hospitalised and community settings. Patients Children and young people (CYP) under age 20 years with laboratory-proven COVID-19. Study review, data extraction and quality Potentially eligible articles were reviewed on title and abstract by one reviewer. Quality was assessed using the modified AMSTARS criteria and data were extracted from included studies by two reviewers. Main outcome measures Prevalence of symptoms and signs of COVID-19. Results 1325 studies were identified and 18 reviews were included. Eight were high quality, 7 medium and 3 low quality. All reviews were dominated by studies of hospitalised children. The proportion of asymptomatic CYP ranged from 14.6% to 42%. Fever and cough were the the most common symptoms; proportions with fever ranged from 46% to 64.2% and with cough from 32% to 55.9%. All other symptoms or signs including rhinorrhoea, sore throat, headache, fatigue/myalgia and gastrointestinal symptoms including diarrhoea and vomiting were infrequent, occurring in less than 10%–20%. Conclusions Fever and cough are the most common symptoms in CYP with COVID-19, with other symptoms infrequent. Further research on symptoms in community samples are needed to inform pragmatic identification and testing programmes for CYP.
Determinants analysis of loan use and repayment behaviour among farmers in Benin: A semi- nonparametric bivariate probit approach

This paper analysed the determinants of the use and repayment behaviour of loans among farmers in Benin. Data were collected from 400 farmers randomly selected from twenty villages‟ representative of the country's seven Agricultural Development Hubs (ADH). The data were analysed using a semi-non parametric bivariate probit approach. The results indicated that there was a relationship between the decision to use the loans and the decision to repay them. In total, nine explanatory variables in the model were significant. Three of these variables (education level, membership of a farmer organization and income) determined with different levels of significance the use of q and default on loan repayment. Five of these variables (age, sex, household size, farm size and contact with extension services) influenced loan use, but had no significant effect on loan repayment. A single variable (asset value) had no effect on loan use, but had significantly affected the repayment of the loan. Based on these results from Benin, MFIs in developing countries should take into account significant variables when concluding contracts with borrowing farmers.
Gibberellic Acid and Presowing Chilling Increase Seed Germination of Indiangrass [Sorghastrum nutans (L.) Nash.]

Following dry storage for 5 or 11 months (new and old seeds, respectively) at 5 °C, less than 10% of the seeds of Indiangrass germinated as determined by a standard germination test. We attempted to increase germination by subjecting seeds to dormancy-breaking treatments, including sodium hypochlorite soak (5.25% v/v NaOCl; 20 or 60 min), prechilling (5 °C for 2 weeks), gibberellic acid during germination (GA 3 , 1000 mg.L -1 ), and combinations thereof. Treatment with NaOCl increased the germination of non-prechilled seeds only when they were germinated in GA 3 ; a 60-min soak in NaOCl increased germination to 53% and 65% in new and old seeds, respectively. Prechilling increased germination to 65% and 47% in new and old seeds, respectively. Germination of new, prechilled seeds was increased further to 86% by either a 20-min soak in NaOCl or germination in GA 3 , Germination of old, prechilled seeds was not promoted further by treatment with NaOCl, but was increased to 67% by germination in GA 3 ; Since NaOCl treatment alone failed to promote germination, we examined the effects on seedling emergence and growth of providing GA 3 at 1000 mg.L -1 during the 2-week prechilling period. While prechilling alone increased emergence to an average 34% for new and old seeds, prechilling with GA 3 increased emergence to 75% and 50% for new and old seeds, respectively. These treatments did not influence seedling shoot dry mass. Seed exposure to GA 3 during rather than after prechilling was more effective in promoting Indiangrass establishment.
Effects of low dosages of lactulose on the intestinal function of healthy adults

Responses to low dosages of lactulose (3 or 5 g/day), focusing on intestinal function and faecal character, were assessed by self-observation in 296 subjects. An increase in defaecation frequency, softening of faeces, a change in faecal colour towards yellow, reduced faecal hardness and slight increases of abdominal gaseous symptoms were observed as a result of lactulose intake in normal adults and in adults who had a defaecation frequency of less than 1.0 per day. In addition, responses to lactulose intake (4 g/day) in terms of faecal flora and profile were analysed in 8 healthy adults. The log 1 0 number of bifidobacteria increased (to 10.3) and the ratio to total bacteria increased (to 50.5%), whereas the corresponding values for Bacteriodaceae and clostridia decreased. Faecal pH and indole concentration decreased. The following trends were also observed: high levels of faecal water and acetic and lactic acids; and low levels of iso-butyric and isovaleric acids, p-cresol, skatole, urease, tryptophanase and others. It is suggested that a low daily intake of lactulose could improve the intestinal environment and ameliorate constipation.
Integration the biologic factors into the staging of breast cancer patients with ipsilateral supraclavicular lymph node metastasis

Purpose: To investigate the accuracy and the discriminatory performance in the prognostic prediction in breast cancer (BC) patients with ipsilateral supraclavicular lymph node (ISLN) metastasis using the between the American Joint Committee on Cancer (AJCC) 7th and 8th edition staging system. Methods: Female patients diagnosed as BC were retrieved from the Surveillance, Epidemiology, and End Results database between 2010 and 2014. Chi-squared test, Kaplan-Meier method, Cox proportional hazard analysis, and the receiver operating characteristics were used to conduct statistical analysis. Results: We included 1097 BC patients with ISLN metastasis (N3c disease), including 29.4% (n=322) and 70.6% (n=775) of patients with non-metastatic and metastatic stage at diagnosis, respectively. In non-metastatic stage patients, 64.9% of the patients categorized as having stage IIIC disease in the 7th edition AJCC staging system were downstaged to stage IIIA or IIIB according to the 8th AJCC staging criteria. The AJCC 8th edition staging system had better discriminatory prognostic value than the 7th AJCC staging (area under the curve: 0.586 vs. 0.577, P=0.0006), with a 5-year breast cancer-specific survival (BCSS) rate of 71.3%, 62.2%, 45.2% and 39.1% in stage IIIA, IIIB, IIIC, and IV cohorts, respectively (P<0.0001). The multivariate prognostic analysis revealed that the AJCC 8th edition staging system was an independent prognostic factor for BCSS, while no statistical difference in BCSS was found between the 8th AJCC stage IIIC and IV patients (P=0.188). Conclusion: The AJCC 8th edition pathological prognostic staging showed a better discriminatory prognostic value in ISLN-metastasized breast cancer patients. An additional clarification strategy in stage IIIC disease based on the 8th AJCC staging should be developed to differentiate patients who are curable with multimodality therapy and patients who have less benefit from curative treatment.
FAUNA PARASITARIA DE JUVENILES DE ARAHUANA, Osteoglossum bicirrhosum (VANDELLI, 1829) CULTIVADOS EN EL CENTRO DE INVESTIGACIONES DE QUISTOCOCHA, LORETO,PERU

La arahuana, Osteoglossum bicirrhosum , es un pez del orden Osteoglossiformes que se distribuye por toda la planicie inundable de la cuenca Amazonica. Puede alcanzar un metro de longitud y pesar hasta cinco kilogramos. Es considerado un predador generalista caracterizado por realizar saltos fuera del agua para capturar presas en el follaje proximo de la zona litoral. Es importante en la pesca comercial, deportiva y acuariofilia. El presente estudio tuvo como objetivo estudiar la fauna parasitaria de 60 juveniles de arahuana cultivados en el Centro de Investigaciones de Quistococha del IIAP. En total fueron identificadas tres especies de parasitos metazoarios infestando a los peces en estudio. Todos los peces analizados presentaron presencia de al menos un parasito metazoario. El mayor porcentaje de prevalencia lo presento el nematodo Camallanus acaudatus (83.33%) y Gonocleithrum cursitans presento el mayor valor de abundancia (10,453 ejemplares por pez).
The Effect of Biomass Pellet Length, Test Conditions and Torrefaction on Mechanical Durability Characteristics According to ISO Standard 17831-1

With the recent increase in biomass pellet consumption, the mechanical degradation of pellets during transport and handling has become more important. ISO standard 17831-1 is an accepted global standard that is commonly used amongst researchers and industries to determine the mechanical durability of pellets. However, the measured mechanical durability sometimes fails to match the certificate accompanying the shipment. In such cases, pellet length specifications are suspected to play a role. This paper studies the effect of pellet length on mechanical durability for various types of commercially produced biomass pellets. In addition, the effect of test conditions and torrefaction on the mechanical durability of biomass pellets has been investigated. To study the effect of pellet length, pellets were classified into three groups: shorter than 15 mm, 15 to 30 mm, and longer than 30 mm, and their length distributions were measured using an in-house image processing tool. Then, the mechanical durability of pellets was measured using ISO standard 17831-1. The mechanical durability results were compared to random-sized pellet samples. To study the effect of test conditions, the mechanical durability test was operated at different time intervals to elucidate the effect of tumbling at different conditions. The results show that the mechanical durability depends highly on the length distribution of the pellets, with a difference between categories of up to 13%. It was also observed that the mechanical durability remains relatively constant after a specific time interval. Based on the results, we highly recommend modifying the current ISO standard to account for the pellet length distribution (PLD).
The Mechanism of Gill Ventilation in the Dogfish and Skate

1. The respiratory movements of the dogfish, Scyliorhinus (Scyllium) canicula (L.), and the ‘skate’, Raia clavata L. (thornback ray), have been studied by the use of cinematographic and mechanotransducer recording methods. Simultaneous determinations of the time-course of pressure changes in the oro-branchial and parabranchial cavities were also made by means of Hansen condenser manometers. 2. In both species movements of the mouth precede those of the spiracular valve and of the branchial region. Adduction and abduction of the branchial region spreads serially from the first to last gill slit in the dogfish, but movements of the individual gill arches are more nearly synchronous in the skate. Opening of the flap valves formed by extensions of the inter-branchial septa are synchronous in both species. 3. Water entering one side of the mouth leaves by the three posterior gill slits of the same side. Water entering the spiracle leaves through the anterior slits of the same side. This separation of flow is less marked in the skate. 4. The pressure curves recorded in all parts of the system have both positive and negative phases with respect to the external medium. The positive phase, associated with closing of the mouth and spiracle, is larger in the oro-branchial than in the parabranchial cavities and vice versa. The time-course of the pressure changes indicates that the flow across the gills is maintained by the action of a pressure pump in front and a suction pump behind. 5. The suction pump plays a more important role than the pressure pump in the skate and its contribution to the flow across the gills is by no means negligible in the dogfish. 6. The differential pressure curves suggest that the flow across the gills is continuous except in the dogfish for a brief period when the gradient is reversed. The absence of this reversal in the skate suggests that the external gill slit openings are controlled by an active mechanism. This is probably an adaptation to bottom-living habit. 7. All these observations relate to animals which are stationary with respect to the water. During swimming at a reasonable speed leopard sharks ( Triakis semifasciata ) have been observed to make few or no respiratory movements, although they immediately ventilate actively on coming to rest at the bottom of the aquarium.
Population subdivision in the tropical spiny lobster Panulirus ornatus throughout its Indo-West Pacific distribution

Many marine species with Indo-West Pacific distributions have been found to have a considerable level of genetic population structuring across this broad region. We investigated mitochondrial DNA diversity throughout the extensive range of the commercially valuable ornate spiny lobster, Panulirus ornatus, which has an unusually lengthy larval period that can last up to six months. In this study, 298 specimens were sampled from 17 locations covering the West Indian Ocean, Western Australia, Southeast Asia, and the Northwest and Southwest Pacific. Based on sequencing of a 461 bp fragment of mitochondrial control region, we found high levels of haplotype diversity (H = 0.99) and overall significant population differentiation (Φst = 0.113, P < 0.001). The West Indian Ocean and Western Australia populations were the most genetically divergent, with little differentiation among the remaining Southeast Asian and West Pacific populations. The Western Australia population showed evidence of being a peripherally isolated population, with significantly lowered effective population size, likely due to the prevailing ocean currents. The present results indicate that genetically distinct stocks of P. ornatus are present in the wild and that historical and present day biogeographic phenomena have likely influenced this population structure. The presence of these divergent stocks has major implications for both management of fisheries and aquaculture breeding programs for this valuable species.