Miracle-dz/UniFAR-FTUs huggingface dataset:
Gaining local accuracy while not losing generality – extending the range of gap model applications

For the study of long-term processes in forests, gap models generally sacrifice accuracy (i.e., simulating system behavior in a quantitatively accurate manner) for generality (i.e., representing a broad range of systems’ behaviors with the same model). We selected the gap model ForClim to evaluate whether the local accuracy of forest succession models can be increased based on a parsimonious modeling approach that avoids the additional complexity of a 3D crown model, thus keeping parameter requirements low. We improved the representation of tree crowns by introducing feedbacks between (i) light availability and leaf area per tree and (ii) leaf area per tree and diameter growth rate to account for the self-pruning in real stands. The local accuracy of the new model, ForClim v2.9. 5, was considerably improved in simulations at three long-term forest research sites in the Swiss Alps, while its generality was maintained as shown in simulations of potential natural vegetation along a broad environmental gradien.
Screening Indian Mustard Genotypes for Phytoremediating Arsenic-Contaminated Soils

Ten Indian mustard (Brassica juncea L.) genotypes were screened for their phytoremediation potential for arsenic (As) contaminated water under laboratory-controlled conditions. The genotypes were grown in a hydroponic chamber for 20 days in 250-mL beakers containing As-contaminated water. During plant development, changes in plant growth, biomass, and total As were evaluated. Of the 10 genotypes (Pusa Agrani, BTO, Pusa Kranti, Pusa Bahar, Pusa Bold, Pusa Basant, Pusa Jai Kisan, Arka Vardhan, Varuna, and Vaibhav) Pusa Jai Kisan was the most effective in phytoremediating As-contaminated water under hydroponic conditions. This will provide new information for Indian mustard genotypes for phytoremediating As-contaminated soils.
Leaf reflectance spectra capture the evolutionary history of seed plants

Summary Leaf reflectance spectra have been increasingly used to assess plant diversity. However, we do not yet understand how spectra vary across the tree of life or how the evolution of leaf traits affects the differentiation of spectra among species and lineages. Here we describe a framework that integrates spectra with phylogenies and apply it to a global dataset of over 16 000 leaf‐level spectra (400–2400 nm) for 544 seed plant species. We test for phylogenetic signal in spectra, evaluate their ability to classify lineages, and characterize their evolutionary dynamics. We show that phylogenetic signal is present in leaf spectra but that the spectral regions most strongly associated with the phylogeny vary among lineages. Despite among‐lineage heterogeneity, broad plant groups, orders, and families can be identified from reflectance spectra. Evolutionary models also reveal that different spectral regions evolve at different rates and under different constraint levels, mirroring the evolution of their underlying traits. Leaf spectra capture the phylogenetic history of seed plants and the evolutionary dynamics of leaf chemistry and structure. Consequently, spectra have the potential to provide breakthrough assessments of leaf evolution and plant phylogenetic diversity at global scales.
New Frontiers in Prostate Cancer Treatment: Are We Ready for Drug Combinations with Novel Agents?

Medical treatment for metastatic castration-resistant prostate cancer (mCRPC) patients has progressively been evolving from a nonspecific clinical approach to genomics-oriented therapies. The scientific community is in fact increasingly focusing on developing DNA damage repair (DDR) defect-driven novel molecules, both as single-agent therapy and in combined treatment strategies. Accordingly, research is under way into combined drug therapies targeting different pathways, e.g. androgen receptor signaling (ARS) and poly (adenosine diphosphate [ADP]-ribose) polymerase (PARP) enzymes, immune checkpoint (IC) and PARP, IC, and ARS, and prostate-specific membrane antigen (PSMA). In an attempt to formulate evolving treatment paradigms in mCRPC patients, here we selected clinical research into patients undergoing therapies with emerging molecules, with particular emphasis towards PARP-, IC-, and PSMA-inhibitors. In order to focus on those molecules and drug combinations most likely to be translated into routine clinical care in the near future, we selected only those clinical studies currently recruiting patients. A PubMed search focusing on the keywords “prostate cancer”, “metastatic castration-resistant prostate cancer”, “DDR pathways”, “ARS inhibitors”, “PARP inhibitors”, “IC inhibitors”, “PSMA-targeting agents”, and “drug combinations” was performed.
Studies on indirect infection of Trypodendron lineatum Oliv. with Beauveria bassiana (Bals.) Vuill.

The transfer of infection of B. bassiana from contaminated male T. lineatum to non‐contaminated females, as well as the effect of B. bassiana treated timber to the breeding activity and the mortality of young beetles in contaminated soil after immigration for hibernation was investigated. Breeding activity of non contaminated females is reduced by 20 % if placed together with contaminated males. Treated timber shows fewer holes of brood systems and less breeding activity than non‐treated one. The beetles were infected to a higher degree if the soil was contaminated and not the timber. Spraying higher concentrations once or lower ones twice gives mortality rates of up to 100%. Application of spore dust gives lower mortality rates than application of water diluted spores if the concentration on the soil surface is the same. Sterile soil shows after spore contamination a higher mortality rate than non‐sterilized soil. Investigations were completed with observations on the migration flights of hibernated beetles in spring, the hatching of young beetles out of the brood systems, their phototactic behaviour and their distribution in the soil after immigration for hibernation.
Immunoreactive Proteins in the Esophageal Gland Cells of Anisakis Simplex Sensu Stricto Detected by MALDI-TOF/TOF Analysis

In plant and animal nematode parasites, proteins derived from esophageal gland cells have been shown to be important in the host-nematodes relationship but little is known about the allergenic potential of these proteins in the genus Anisakis. Taking into account the increase of anisakiasis and allergies related to these nematodes, immunoreactive properties of gland cell proteins were investigated. Two hundred ventricles were manually dissected from L3 stage larvae of Aniskakis simplex s.s. to allow direct protein analysis. Denaturing gel electrophoresis followed by monochromatic silver staining which revealed the presence of differential (enriched) proteins when compared to total nematode extracts. Such comparison was performed by means of 1D and 2D electrophoresis. Pooled antisera from Anisakis spp. -allergic patients were used in western blots revealing the presence of 13 immunoreactive bands in the ventricular extracts in 1D, with 82 spots revealed in 2D. The corresponding protein bands and spots were excised from the silver-stained gel and protein assignation was made by MALDI-TOF/TOF. A total of 13 (including proteoforms) were unambiguously identified. The majority of these proteins are known to be secreted by nematodes into the external environment, of which three are described as being major allergens in other organisms with different phylogenetic origin and one is an Anisakis simplex allergen.
Phenolic compounds in coffee

Phenolic compounds are secondary metabolites generally involved in plant adaptation to environmental stress conditions. Chlorogenic acids (CGA) and related compounds are the main components of the phenolic fraction of green coffee beans, reaching levels up to 14 % (dry matter basis). These compounds have a number of beneficial health properties related to their potent antioxidant activity as well as hepatoprotective, hypoglycemic and antiviral activities. The main groups of CGA found in green coffee beans include caffeoylquinic acids, dicaffeoylquinic acids, feruloylquinic acids, p-coumaroylquinic acids and mixed diesters of caffeic and ferulic acids with quinic acid, each group with at least three isomers. During coffee processing, CGA may be isomerized, hydrolyzed or degraded into low molecular weight compounds. The high temperatures of roasting also produce transformation of part of CGA into quinolactones and, along with other compounds, melanoidins. This review focuses on the chemical characteristics, biosynthesis, and distribution of CGA and related compounds in coffee. The influence of genetic, physiological and environmental factors as well as processing on the chemical composition of coffee beans is discussed. The impact of CGA composition of green coffee on cup quality is also approached. Despite the existence of substantial published information on the total levels of CGA in coffee, more research is needed on the composition of minor phenolic compounds and specific CGA isomers (and related substances) in green and roasted coffee beans, as well as their impact on coffee quality.
Towards Visual Dialog for Radiology

Current research in machine learning for radiology is focused mostly on images. There exists limited work in investigating intelligent interactive systems for radiology. To address this limitation, we introduce a realistic and information-rich task of Visual Dialog in radiology, specific to chest X-ray images. Using MIMIC-CXR, an openly available database of chest X-ray images, we construct both a synthetic and a real-world dataset and provide baseline scores achieved by state-of-the-art models. We show that incorporating medical history of the patient leads to better performance in answering questions as opposed to conventional visual question answering model which looks only at the image. While our experiments show promising results, they indicate that the task is extremely challenging with significant scope for improvement. We make both the datasets (synthetic and gold standard) and the associated code publicly available to the research community.
Animal Cell Cultures: Risk Assessment and Biosafety Recommendations

During the last three decades, animal cell culturing has been essential for biomedical research and biotechnological activities in general. Along with this increasing importance, biosafety concerns have pointed to the risks of manipulating animal cell cultures for human health and the environment. A maximal reduction of these risks necessitates a thorough risk assessment of the cell cultures used. It involves an evaluation of both the intrinsic properties of the cell culture, including subsequent properties acquired as a result of genetic modification, and the possibility that the cell culture may inadvertently or deliberately become contaminated with pathogens. The latter is a major hazard associated with the manipulation of animal cell cultures, as adventitious agents may be pathogenic and have a better capacity to survive in unfavorable conditions. Consequently, most of the containment measures primarily aim at protecting cells from adventitious contamination. Therefore, a comprehensive evaluation of the risks encountered during the handling of cell cultures should include considerations regarding the type of manipulation as well. As a rule, cell cultures known to harbor an infectious etiologic agent should be manipulated in compliance with containment measures recommended for the etiologic agent. With the exception of very well-characterized cell cultures for which the use of a type II biosafety cabinet depends on the origin of the cells, work with cell cultures from human or primate origin should generally and minimally be performed under containment level 2 using a type II biosafety cabinet. In every case, containment measures should minimize adventitious contamination of the cell cultures and offer a maximal protection of human health and the environment.
Oxygen Consumption During the Life Cycles of the Prepupa-Wintering Bee Megachile rotundata and the Adult-Wintering Bee Osmia lignaria (Hymenoptera: Megachilidae)

Abstract We studied the oxygen consumption of two megachilid bees (Hymenoptera: Megachilidae), Megachile rotundata (F.) and Osmia lignaria Say, at selected, biologically relevant intervals throughout their respective life cycles. The U-shaped oxygen consumption curve and the static weights of wintering (nonfeeding) prepupae that we observed during the life cycle of M. rotundata support previous arguments for a winter diapause similar to that observed in other Hymenoptera. For O. lignaria, which overwinters as an adult, we found stepwise increases in oxygen consumption and continuous weight loss throughout the wintering period. However, our observations on adult O. lignaria wintering requirements are consistent with the previously published results for overwintering M. rotundata prepupae and reveal sharply increasing survival rates when wintered for a minimum of 3 mo. We interpret the greatly reduced survival in both M. rotundata and O. lignaria, as an indication that a critical biological process, diapause, is disrupted among individuals wintered for <3 mo. In the continued development of these two species as commercial scale pollinators on an ever-increasing list of target crops, any similarities or contrasts observed between the “summer bee,” M. rotundata, and the “spring bee,” O. lignaria, although of interest from a biological perspective, will probably have important implications in the continued development of sustainable population management protocols.
Factor analysis of the COVID-19 Perceived Risk Scale: A preliminary study

Abstract This study adapted an 8-item COVID-19 Perceived Risk Scale (CPRS) to assess COVID-19 related personal risk. The sample comprised 3,109 Turkish adults (49.98% males; Meanage = 38.64 ± 10.40). Exploratory and confirmatory factor analyses confirmed a two-factor structure (cognitive and emotional dimensions), with satisfactory reliability. The subscales were correlated with severity and self-efficacy related to COVID-19 and mental health. Women reported higher levels of emotional risk, overall risk, and severity than men. Findings indicate that the CPRS is a psychometrically-sound scale for assessing COVID-19 related perceived risk. The scale can be used to assess people who are vulnerable to the risk of COVID-19.
Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.
Functional and molecular characteristics of rice and barley NIP aquaporins transporting water, hydrogen peroxide and arsenite

Mercury-sensitive water transport activities were detected in seven NIP (Nodulin 26-like intrinsic protein) type aquaporins among eleven NIPs examined. Amino acid substitutions in rice OsNIP3;3 revealed that mercury-sensitivity depended on a histidine (but not on a cysteine) in apoplastic loop C in plant NIP aquaporins, although the cysteine is involved in the mercury-sensitivity of animal aquaporins. Rice OsNIP3;3 was also first identified as a unique aquaporin facilitating all water, hydrogen peroxide and arsenite transports. In rice OsNIP3;2, hydrogen peroxide and arsenite transport activities were detected, but water transport was not. Barley HvNIP1;2or rice OsNIP2;1-expressing yeast cells showed the arsenite transport activity but not the H2O2 transport activity. The present work revealed novel molecular mechanisms of water and other low molecular weight compounds transport/selection in barley and rice NIP aquaporins, including the histidine-related mercury-sensitivity in the water transport of aquaporins.
Isolation and characterization of Streptococcus spp. group B in Nile tilapias (Oreochromis niloticus) reared in hapas nets and earth nurseries in the northern region of Parana State, Brazil

The objective of this study was to isolate and characterize Streptococcus spp. in Nile tilapias (Oreochromis niloticus) reared in net-pens and earth nurseries. Eight intensive tilapia-rearing farms were investigated in north Parana, Brazil from April 1st 2001 to April 30th 2002. The fish were reared in a system of hapas nets on four farms and in earth nurseries on other four farms. A total of 370 samples were analyzed of material collected from 120 fish (brain, liver, kidney, skin scrapes, ascites liquid and eye) that were sown on BHI agar (Brain Heart Infusion) supplemented with 1% yeast extract and sheep blood. Streptococcus spp. was isolated in 36 of the samples (18 brain, eight liver, eight kidney and two ascites liquid) from 25 fish. Streptococci were isolated in both systems, almost in the same proportion. First the streptococci were characterized by the catalase and esculin test, growth in methylene blue and sodium chloride at 6.5%. They were classified in groups by the Slidex Strepto-Kit (BioMerieux, France). The phenotypic characteristics were determined by the Api 20 Strep microtest system (BioMerieux, France). The 36 Streptococcus spp. samples did not present hemolysis and were classified as Lancefield group B. Further 16 samples were identified as Streptococcus agalactiae and 20 were not identified by the Api 20 Strep, but presented the same biochemical profile described for the reference strain of Streptococcus difficile (ND-2-22).
Evaluation of heat-induced changes in Spanish commercial milk: hydroxymethylfurfural and available lysine content

Summary Hydroxymethyfurfural (HMF) content and loss of available lysine were measured asindices of heat damage in various Spanish commercial milks (pasteurized, UHT sterilizedand in-bottle sterilized milks) with similar processing dates. HMF level was determinedby the traditional colorimetric procedure and by the reversed-phase HPLC method.Available lysine was measured by an alternative method with o-phthaldialdehyde asXuorescent marker. A signiWcative relationship has been found between the HMF con-tent and loss of available lysine and both are suitable for use as heat-induced indices.When loss of lysine (y) was expressed as percentage and HMF (x) as m M , the functionof the correlation line was, y 5 0.47x2 0.089 (r 5 0.958, P , 0.005). Keywords Heat damage, process identiWcation, rapid analysis. Introduction The principal heat treatments applied to milksuch as pasteurization, UHT sterilization and in-bottle sterilization, are designed to guaranteepreservation of milk through the destruction ofmicroorganisms and the inactivation of enzymesthat may reduce its shelf-life (Burton, 1984). However, industrial heat processing inevitablycauses chemical changes in milk, particularlywhen milk is overheated. Among other chemi-cal/physical changes which can signiWcantly aVectthe nutritional and sensorial quality of a product(Baltes, 1982), one of the reactions that takesplace during heating and storage of milk is the so-called Maillard reaction (MR). MR involves thefree amino residues of proteins, mainly the e-amino group of lysine, and reducing carbohy-drates, which leads to amino acid sugar reactionproducts (Hodge, 1953). During industrial treat-ment of liquid milk, the MR usually does notproceed to the point of production ofmelanoidins; it is limited to the formation oflactulosyllysine (DLL), a stable Amadori product,bound to the protein in the early stage (Finot et al., 1977; Bujard & Finot, 1978). The forma-tion of DLL has an important nutritionalsigniWcance because it reduces the biologicalavailability of lysine in milk and milk products(Moller et al., 1977). Protein-bound DLL ispartially converted by acid hydrolysis intofurosine. Determination of furosine gives aindirect value of lysine blocked as Amadoriproduct if the conversion rate is known.Estimation of lysine loss has provided a directmeans of obtaining information about the extentof the initial stages of the MR. Several chemicalmethods have been used to estimate the bioavail-able lysine content of food proteins (Hurrell etal., 1983). Variable results have been obtainedwhen these methods are applied to proteinssubjected to early Maillard browning reactionbecause the presence of DLL in proteins mayresult in an overestimation of the available lysinecontent, depending on the chemical methodemployed (Hurrell & Carpenter, 1981). Alterationof the number of primary amino groups of