Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid assessment and prediction of the efficiency of two preservatives against S. aureus in cosmetic products using High Content Screening—Confocal Laser Scanning Microscopy

Most cosmetic products are susceptible to microbiological spoilage due to contaminations that could happen during fabrication or by consumer’s repetitive manipulation. The composition of cosmetic products must guarantee efficient bacterial inactivation all along with the product shelf life, which is usually assessed by challenge-tests. A challenge-test consists in inoculating specific bacteria, i.e. Staphylococcus aureus, in the formula and then investigating the bacterial log reduction over time. The main limitation of this method is relative to the time-consuming protocol, where 30 days are needed to obtain results. In this study, we have proposed a rapid alternative method coupling High Content Screening—Confocal Laser Scanning Microscopy (HCS-CLSM), image analysis and modeling. It consists in acquiring real-time S. aureus inactivation kinetics on short-time periods (typically 4h) and in predicting the efficiency of preservatives on longer scale periods (up to 7 days). The action of two preservatives, chlorphenesin and benzyl alcohol, was evaluated against S. aureus at several concentrations in a cosmetic matrix. From these datasets, we compared two secondary models to determine the logarithm reduction time (Dc) for each preservative concentration. Afterwards, we used two primary inactivation models to predict log reductions for up to 7 days and we compared them to observed log reductions. The IQ model better fits datasets and the Q value gives information about the matrix level of interference.
Hyperpolarization of Nitrile Compounds Using Signal Amplification by Reversible Exchange

Signal Amplification by Reversible Exchange (SABRE), a hyperpolarization technique, has been harnessed as a powerful tool to achieve useful hyperpolarized materials by polarization transfer from parahydrogen. In this study, we systemically applied SABRE to a series of nitrile compounds, which have been rarely investigated. By performing SABRE in various magnetic fields and concentrations on nitrile compounds, we unveiled its hyperpolarization properties to maximize the spin polarization and its transfer to the next spins. Through this sequential study, we obtained a ~130-fold enhancement for several nitrile compounds, which is the highest number ever reported for the nitrile compounds. Our study revealed that the spin polarization on hydrogens decreases with longer distances from the nitrile group, and its maximum polarization is found to be approximately 70 G with 5 μL of substrates in all structures. Interestingly, more branched structures in the ligand showed less effective polarization transfer mechanisms than the structural isomers of butyronitrile and isobutyronitrile. These first systematic SABRE studies on a series of nitrile compounds will provide new opportunities for further research on the hyperpolarization of various useful nitrile materials.
Production of Iron Enriched Eggs of Laying Hens

An experiment was conducted to investigate the efficiency of transfer of dietary iron sources to eggs of laying hens. Eighty ISA-Brown laying birds of 30 wk old were housed in 40 cages of 2 birds each. Eight birds in four cages were assigned to one of the following ten treatments: T1; control, T2; 100 ppm iron supplementation with iron-methionine chelate (Fe-Met-100), T3; Fe-Met- 200, T4; Fe-Met-300, T5; 100 ppm iron supplementation with iron sulfate (FeSO4-100), T6; FeSO4-200, T7; FeSO4-300, T8; 100 ppm iron supplementation with Availa-Fe  (Availa-Fe-100), T9; Availa-Fe-200 and T10; Availa-Fe-300. Results of 40 d feeding trial showed that there were no consistent responses in laying performance by source and level of iron supplementation. However, eggshell strength and color were improved by Fe supplementation. Egg iron content was maximized at 10-15 days after feeding supplemental Fe. Fe- Met was the most effective source in enriching Fe of eggs followed by Availa-Fe and FeSO4. Increasing supplementary Fe level more than 100 ppm was not effective in Fe-Met and Availa-Fe treatments. Average Fe enrichment of 18% was achieved after feeding Fe-Met-100 for 15 d. In conclusion, enrichment of Fe in egg could be effectively achieved by supplementation of Fe-Met-100 for 15 d. (Asian-Aust. J. Anim. Sci. 2004. Vol 17, No. 12 : 1725-1728)
GENETIC ANALYSES OF ATLANTIC NORTHERN BLUEFIN TUNA POPULATIONS

SUMMARY In recent years, there has been considerable debate about whether the Atlantic northern bluefin tuna (Thunnus thynnus) exist as a panmictic unit. This question is addressed by examining both mitochondrial DNA control region nucleotide sequences and nuclear gene ldhA allele frequencies in replicate samples of northern bluefin tuna from the Mediterranean Sea and the northwestern Atlantic Ocean. Preliminary analyses of both the ldhA and the mtDNA data had provided tentative evidence for population subdivision of Atlantic northern bluefin tuna. However, with increased sample sizes, AMOVA analyses of both types of data revealed no significant differences between samples from the two regions. Similarly, pairwise comparisons of multiple year class samples from the two regions provided no evidence for population subdivision. These results demonstrate the importance of analyzing multiple year classes and large sample sizes in stock structure analyses. Also, it is important to note that failure to find genetic evidence for population substructure does not constitute evidence for a single panmictic population. Multiple subpopulations could exist, and genetic differentiation could be prevented by large population sizes and/or low levels of migration. RESUME
Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus californianus) with Polyserositis and Steatitis

An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Histologically, affected tissues had extensive accumulations of macrophages with perivascular lymphocytes, plasma cells, and fewer neutrophils. Using viral metagenomics on a mesenteric lymph node six mammalian viruses were identified consisting of novel parvovirus, polyomavirus, rotavirus, anellovirus, and previously described Csl adenovirus 1 and Csl bocavirus 4. The causal or contributory role of these viruses to the gross and histologic lesions of this sea lion remains to be determined.
Kinetically distinct processing pathways diversify the CD8+ T cell response to a single viral epitope

Significance CD8+ T cells eliminate infections and cancers through recognition of antigen-derived peptides displayed at the cell surface in combination with MHC class I molecules. We show that a single glycoprotein-derived epitope is generated from two sources: 1) the conventional cohort that is delivered to the endoplasmic reticulum, a fraction failing quality control and undergoing ERAD, and 2) an exceedingly minor fraction that is mislocalized to the cytosol during translation and immediately degraded. Notably, peptide derived from mislocalized antigen is delivered to the cell surface with faster kinetics and drives greater CD8+ T cell expansion and functionality. These findings provide key insights for development of vaccines intended to elicit CD8+ T cell-mediated protection. The source proteins from which CD8+ T cell-activating peptides are derived remain enigmatic. Glycoproteins are particularly challenging in this regard owing to several potential trafficking routes within the cell. By engineering a glycoprotein-derived epitope to contain an N-linked glycosylation site, we determined that optimal CD8+ T cell expansion and function were induced by the peptides that are rapidly produced from the exceedingly minor fraction of protein mislocalized to the cytosol. In contrast, peptides derived from the much larger fraction that undergoes translocation and quality control are produced with delayed kinetics and induce suboptimal CD8+ T cell responses. This dual system of peptide generation enhances CD8+ T cell participation in diversifying both antigenicity and the kinetics of peptide display.
Biased hate crime perceptions can reveal supremacist sympathies

Significance Some mass shooters openly express intent to target ethnic and racial minorities, but members of the public still do not agree on whether the gunman was indeed motivated by prejudice and/or hatred. The present research finds that members of a dominant majority often express uncertainty about hate crimes when they privately sympathize with the perpetrator’s cause; specifically, aggrieved members of a dominant majority do not want to acknowledge the victimhood of minority groups. The tendency to deemphasize hate crimes can be traced back to each individual’s own frustrations with society and resentment of other groups. Ultimately, the same general process that explains support for violent extremism, around the world, may also explain supremacist sympathies in modern Western democracies. People may be sympathetic to violent extremism when it serves their own interests. Such support may manifest itself via biased recognition of hate crimes. Psychological surveys were conducted in the wakes of mass shootings in the United States, New Zealand, and the Netherlands (total n = 2,332), to test whether factors that typically predict endorsement of violent extremism also predict biased hate crime perceptions. Path analyses indicated a consistent pattern of motivated judgment: hate crime perceptions were directly biased by prejudicial attitudes and indirectly biased by an aggrieved sense of disempowerment and White/Christian nationalism. After the shooting at a synagogue in Pittsburgh, Pennsylvania, disempowerment-fueled anti-Semitism predicted lower perceptions that the gunman was motivated by hatred and prejudice (study 1). After the shootings that occurred at two mosques in Christchurch, New Zealand, disempowerment-fueled Islamoprejudice similarly predicted lower hate crime perceptions (study 2a). Conversely, after the tram shooting in Utrecht, Netherlands (which was perpetrated by a Turkish-born immigrant), disempowerment-fueled Islamoprejudice predicted higher hate crime perceptions (study 2b). Finally, after the Walmart shooting in El Paso, Texas, hate crime perceptions were specifically biased by an ethnonationalist view of Hispanic immigrants as a symbolic (rather than realistic) threat to America; that is, disempowered individuals deemphasized likely hate crimes due to symbolic concerns about cultural supremacy rather than material concerns about jobs or crime (study 3). Altogether, biased hate crime perceptions can be purposive and reveal supremacist sympathies.
Caffeine improves performance but not duration of the countermovement jump phases.

BACKGROUND The countermovement jump (CMJ) test is often employed to assess power generated in the lower limbs and has been related to performance in several sports modalities. The objective of this study was to assess the effects of caffeine supplementation on jump height, average power (AP), peak power (PP), maximum velocity (Vmax), force production and duration of the eccentric, isometric and concentric muscle contraction phases of a CMJ. METHODS Sixteen resistance-trained men (age: 22.69 ± 2.12 years; height: 1.78 ± 0.06 m; weight: 78.09 ± 10.27 kg) performed a CMJ 60 minutes after having taken an oral supplement containing 6 mg·kg-1 of caffeine or placebo (sucrose). The study design was randomized, double-blind crossover. RESULTS Caffeine ingestion improved jump height (+3.86%, p=0.02), Vmax (+1.49%, p=0.023), AP (+4.83%, p=0.006), and PP (+3.49%, p=0.004). CONCLUSIONS Acute caffeine supplementation leads to improved CMJ height, Vmax, AP and PP without significantly affecting the duration of the different test phases. Therefore, caffeine supplementation may be employed as ergogenic aid in sports where CMJ performance has been associated with sport-specific performance enhancements.
Allometry of the leg muscles of mammals

Measurements have been made of the leg muscles of mammals ranging from shrews Sorex to an elephant Loxodonta. Allometric equations based on body mass have been calculated for muscle masses, fibre lengths and moment arms and the thickness of a tendon, in several groups of mammals. Departures from geometric similarity in mammals in general (excluding bipedal hoppers) are noted and discussed. Differences between primates; fissipedes, bovids and bipedal hoppers are also demonstrated.
Route planning for hazardous materials transportation: Multi-criteria decision-making approach

Transport of hazardous material (THM) represents a complex area involving a large number of participants. The imperative of THM is minimization of risks in the entire process of transportation from the aspect of everyone involved in it, which is not an easy task at all. To achieve this, it is necessary in its early phase to carry out adequate evaluation and selection of an optimal transport route. In this paper, optimal route criteria for THM are selected using a new approach in the field of multi-criteria decision-making. Weight coefficients of these criteria were determined by applying the Full Consistency Method (FUCOM). Evaluation and selection of suppliers is determined by applying the TOPSIS (Technique for Order of Preference by Similarity to Ideal Solution) and the MABAC (Multi-attributive Border Approximation Area Comparison) methods. In order to establish the stability of models and validate the results obtained from the FUCOM-TOPSIS-MABAC model, a sensitivity analysis (of ten different scenarios) was performed. The sensitivity analysis implied changes of the weight coefficients criteria with respect to their original value. The proposed route model was tested on the real example of the transport Eurodiesel in Serbia.
Supporting tailoring of complex product development processes: An approach based on structural modelling and analysis

Project tailoring is discussed in academia and industry as a way to bridge the project-specific adaptation of generic organizational reference process models. Research into process tailoring in interdisciplinary product development is currently limited. We have developed a structure-based approach for supporting process tailoring, addressing limitations in existing approaches through: Concrete method support; systematic analysis of documented tailoring knowledge using structural analysis; and social aspects, e.g. stakeholder inclusion. The approach has been evaluated in eight case studies.
Elevated energy requirement of cone photoreceptors

Significance From recent measurements of mammalian cone physiology, we have calculated cone ATP utilization in darkness and in the light. We show that single cones consume ATP at a much higher rate than single rods, a difference that is greatly increased during the day. This high metabolic rate is especially prominent in the primate fovea, which may make this part of the human eye particularly sensitive to decreases in glucose uptake or other metabolic alterations. We have used recent measurements of mammalian cone light responses and voltage-gated currents to calculate cone ATP utilization and compare it to that of rods. The largest expenditure of ATP results from ion transport, particularly from removal of Na+ entering outer segment light-dependent channels and inner segment hyperpolarization-activated cyclic nucleotide-gated channels, and from ATP-dependent pumping of Ca2+ entering voltage-gated channels at the synaptic terminal. Single cones expend nearly twice as much energy as single rods in darkness, largely because they make more synapses with second-order retinal cells and thus must extrude more Ca2+. In daylight, cone ATP utilization per cell remains high because cones never remain saturated and must continue to export Na+ and synaptic Ca2+ even in bright illumination. In mouse and human retina, rods greatly outnumber cones and consume more energy overall even in background light. In primates, however, the high density of cones in the fovea produces a pronounced peak of ATP utilization, which becomes particularly prominent in daylight and may make this part of the retina especially sensitive to changes in energy availability.
PIRADS Category as a Predictor of Progression to Unfavorable Risk Prostate Cancer in Men on Active Surveillance.

PURPOSE To identify baseline imaging and clinical characteristics of patients that may improve risk stratification among patients being evaluated for active surveillance (AS). MATERIALS AND METHODS From July 2007 to January 2020, patients referred to our institution for prostate cancer were evaluated and those that remained on AS were identified. Men underwent multiparametric MRI (mpMRI) upon entry into our AS protocol during which baseline demographic and imaging data were documented. Patients were then followed and outcomes, specifically progression to ≥GG3 disease, were recorded. RESULTS Of the men placed on AS, 344 men had at least one PIRADS score documented. For those with an index lesion PIRADS category of 5, 33% patients (17/51) progressed to ≥GG3 on AS with a median time to progression of 31 months. When comparing the progression-free survival times and progression rates in each category, the PIRADS category was found to be associated with progression to ≥GG3 on AS (p<0.01). On univariable analysis, factors associated with progression included an index lesion PIRADS category of 5, PSAD, and the size of the largest lesion. On multivariable analysis, only PIRADS category of 5 and PSAD were found to be associated with progression on AS. CONCLUSION PIRADS lesion categories at baseline mpMRI during AS enrollment can be used to predict cancer progression to GG3 cancer on AS. This information, along with other clinical data, can better assist urologists in identifying and managing patients appropriate for active surveillance.
Early Embryonic Expression of AP-2α Is Critical for Cardiovascular Development

Congenital cardiovascular malformation is a common birth defect incorporating abnormalities of the outflow tract and aortic arch arteries, and mice deficient in the transcription factor AP-2α (Tcfap2a) present with complex defects affecting these structures. AP-2α is expressed in the pharyngeal surface ectoderm and neural crest at mid-embryogenesis in the mouse, but the precise tissue compartment in which AP-2α is required for cardiovascular development has not been identified. In this study we describe the fully penetrant AP-2α deficient cardiovascular phenotype on a C57Bl/6J genetic background and show that this is associated with increased apoptosis in the pharyngeal ectoderm. Neural crest cell migration into the pharyngeal arches was not affected. Cre-expressing transgenic mice were used in conjunction with an AP-2α conditional allele to examine the effect of deleting AP-2α from the pharyngeal surface ectoderm and the neural crest, either individually or in combination, as well as the second heart field. This, surprisingly, was unable to fully recapitulate the global AP-2α deficient cardiovascular phenotype. The outflow tract and arch artery phenotype was, however, recapitulated through early embryonic Cre-mediated recombination. These findings indicate that AP-2α has a complex influence on cardiovascular development either being required very early in embryogenesis and/or having a redundant function in many tissue layers.
Network-based approaches for understanding gene regulation and function in plants.

Expression reprogramming directed by transcription factors (TFs) is a primary gene regulation underlying most aspects of the biology of any organism. Our views of how gene regulation is coordinated are dramatically changing thanks to the advent and constant improvement of high-throughput profiling and transcriptional network inference methods: from activities of individual genes to functional interactions across genes. These technical and analytical advances can reveal the topology of transcriptional networks in which hundreds of genes are hierarchically regulated by multiple TFs at a systems-level. Here we review the state of the art of experimental and computational methods used in plant biology research to obtain large-scale datasets and model transcriptional networks. Examples of direct use of these network models and perspectives on their limitations and future directions are also discussed.
A graph-based method for reconstructing entities from coordination ellipsis in medical text

OBJECTIVE Coordination ellipsis is a linguistic phenomenon abound in medical text and is challenging for concept normalization because of difficulty in recognizing elliptical expressions referencing 2 or more entities accurately. To resolve this bottleneck, we aim to contribute a generalizable method to reconstruct concepts from medical coordinated elliptical expressions in a variety of biomedical corpora. MATERIALS AND METHODS We proposed a graph-based representation model and built a pipeline to reconstruct concepts from coordinated elliptical expressions in medical text (RECEEM). There are 4 modules: (1) identify all possible candidate conjunct pairs from original coordinated elliptical expressions, (2) calculate coefficients for candidate conjuncts using the embedding model, (3) select the most appropriate decompositions by global optimization, and (4) rebuild concepts based on a pathfinding algorithm. We evaluated the pipeline's performance on 2658 coordinated elliptical expressions from 3 different medical corpora (ie, biomedical literature, clinical narratives, and eligibility criteria from clinical trials). Precision, recall, and F1 score were calculated. RESULTS The F1 scores for biomedical publications, clinical narratives, and research eligibility criteria were 0.862, 0.721, and 0.870, respectively. RECEEM outperformed 2 previously released methods. By incorporating RECEEM into 2 existing NLP tools, the F1 scores increased from 0.248 to 0.460 and from 0.287 to 0.630 on concept mapping of 1125 coordination ellipses. CONCLUSIONS RECEEM improves concept normalization for medical coordinated elliptical expressions in a variety of biomedical corpora. It outperformed existing methods and significantly enhanced the performance of 2 notable NLP systems for mapping coordination ellipses in the evaluation. The algorithm is open sourced online (https://github.com/chiyuan1126/RECEEM).
Melioidosis and the Heart: A Systematic Review

Melioidosis is caused by Gram-negative bacterium Burkholderia pseudomallei. Clinical presentation can vary from pneumonia, sepsis and multi-focal abscess formation. The aim of this study was to systemically review the cardiac manifestations of melioidosis in the literature and describe their epidemiology, microbiological diagnosis and outcomes. A systematic review of the peer-reviewed literature was carried out in PubMed and Google Scholar for human melioidosis cases with cardiac involvement. Quantitative data for cases of melioidosis were obtained, including age, sex, microbiological diagnosis, treatment, and outcome. 980 articles were screened, of which 31 articles were eligible. The most common cardiac site of infection was pericarditis, followed by endocarditis and myocarditis. Over 95% of cardiac involvement occurred in males, and mortality was the lowest in pericarditis and highest in myocarditis. Valvular vegetations were all small, left-sided, and did not require surgery. Antibiotic treatment included a bactericidal induction therapy with ceftazidime or a carbapenem ± TMP-SMX, followed by eradication therapy with TMP–SMX in most patients as previously established. In conclusion, melioidosis varies in clinical presentation and is also known as a great imitator. Although cardiac involvement is rare, this is the first systematic review to summarise all cases reported in the literature to date.