Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethanol from Lignocellulose - Fermentation Inhibitors, Detoxification and Genetic Engineering of Saccharomyces cerevisiae for Increased Resistance

Ethanol can be produced from lignocellulose by first hydrolysing the material to sugars, and then fermenting the hydrolysate with the yeast Saccharomyces cerevisiae. Hydrolysis using dilute sulphuric acid has advantages over other methods, however, compounds which inhibit fermentation are generated during this kind of hydrolysis. The inhibitory effect of aliphatic acids, furans, and phenolic compounds was investigated. The generation of inhibitors during hydrolysis was studied using Norway spruce as raw material. It was concluded that the decrease in the fermentability coincided with increasing harshness of the hydrolysis conditions. The decrease in fermentability was not correlated solely to the content of aliphatic acids or furan derivatives. To increase the fermentability, detoxification is often employed. Twelve detoxification methods were compared with respect to the chemical composition of the hydrolysate and the fermentability after treatment. The most efficient detoxification methods were anion-exchange at pH 10.0, overliming and enzymatic detoxification with the phenol-oxidase laccase. Detailed analyses of ion exchange revealed that anion exchange and unspecific hydrophobic interactions greatly contributed to the detoxification effect, while cation exchange did not. The comparison of detoxification methods also showed that phenolic compounds are very important fermentation inhibitors, as their selective removal with laccase had a major positive effect on the fermentability. Selected compounds; aliphatic acids, furans and phenolic compounds, were characterised with respect to their inhibitory effect on ethanolic fermentation by S. cerevisiae. When aliphatic acids or furans were compared, the inhibitory effects were found to be in the same range, but the phenolic compounds displayed widely different inhibitory effects. The possibility of genetically engineering S. cerevisiae to achieve increased inhibitor resistance was explored by heterologous expression of laccase from Trametes versicolor and by homologous overexpression of phenylacrylic acid decarboxylase. Both procedures resulted in S. cerevisiae transformants displaying increased resistance towards lignocellulose-derived aromatic compounds. (Less)
Microfluidic platform for integrated plasmonic detection in laminal flow

In this work, we propose a novel approach to design robust microfluidic devices with integrated plasmonic transducers allowing portability, reduced analysis time through dynamic measurements and high sensitivity. Specifically, the strategy we apply involves two steps: (i) the controlled deposition of gold bipyramidal nanoparticles (AuBPs) onto a functionalized solid glass substrate and (ii) the integration of the as-fabricated plasmonic substrate into a polydimethylsiloxane (PDMS) microfluidic circuit. The localized surface plasmon resonance (LSPR) sensitivity of the plasmonic-microfluidic device was evaluated by monitoring the optical responses at refractive index changes, proving a bulk sensitivity of 243 nm RIU−1 for the longitudinal LSPR band of isolated AuBPs and 150 nm RIU−1 for the band assigned to end-to-end linked nanoparticles. A strong electric field generated in the gaps between AuBPs—due to the generation of the so-called extrinsic ‘hot-spots’—was subsequently proved by the volumetric surface enhanced Raman scattering (SERS) detection of molecules in continuous flow conditions by loading the analyte into the microfluidic channel via a syringe pump. In conclusion, our miniaturized portable microfluidic system aims to detect and identify, in real-time with high accuracy, analyte molecules in laminal flow, thus providing a groundwork for further complex biosensing applications.
Thymol Protects Channel Catfish from Aeromonas hydrophila Infection by Inhibiting Aerolysin Expression and Biofilm Formation

Aeromonas hydrophila is an opportunistic pathogen responsible for a number of diseases in freshwater farming. Moreover, the bacterium has been identified as a zoonotic pathogen that threatens human health. Antibiotics are widely used for treatments of infectious diseases in aquaculture. However, the abuse of antibiotics has led to the emergence of antimicrobial resistant strains. Thus, novel strategies are required against resistant A. hydrophila strains. The quorum sensing (QS) system, involved in virulence factor production and biofilm formation, is a promising target in identifying novel drugs against A. hydrophila infections. In this study, we found that thymol, at sub-inhibitory concentrations, could significantly reduce the production of aerolysin and biofilm formation by inhibiting the transcription of genes aerA, ahyI, and ahyR. These results indicate that thymol inhibits the quorum sensing system. The protective effects of thymol against A. hydrophila mediated cell injury were determined by live/dead assay and lactate dehydrogenase (LDH) release assay. Moreover, the in vivo study showed that thymol could significantly decrease the mortality of channel catfish infected with A. hydrophila. Taken together, these findings demonstrate that thymol could be chosen as a phytotherapeutic candidate for inhibiting quorum sensing system-mediated aerolysin production and biofilm formation in A. hydrophila.
Revealing Fungal Communities in Alpine Wetlands through Species Diversity, Functional Diversity and Ecological Network Diversity

The biodiversity of fungi, which are extremely important in maintaining the ecosystem balance in alpine lakeside wetlands, has not been fully studied. In this study, we investigated the fungal communities of three lakeside wetlands from different altitudes in the Qinghai–Tibet Plateau and its edge. The results showed that the fungi of the alpine lakeside wetland had higher species diversity. Functional annotation of fungi by FUNGild software showed that saprophytic fungi were the most abundant type in all three wetlands. Further analysis of the microbial phylogenetic molecular ecological network (pMEN) showed that saprophytic fungi are important species in the three wetland fungal networks, while symbiotic fungi and pathotrophic fungi have different roles in the fungal networks in different wetlands. Community diversity was high in all three lakeside wetlands, but there were significant differences in the composition, function and network structure of the fungal communities. Contemporary environmental conditions (soil properties) and historical contingencies (geographic sampling location) jointly determine fungi community diversity in this study. These results expand our knowledge of fungal biodiversity in the alpine lakeside wetlands.
Buparlisib in combination with tamoxifen in pretreated patients with hormone receptor‐positive, HER2‐negative advanced breast cancer molecularly stratified for PIK3CA mutations and loss of PTEN expression

The PIKTAM study evaluated the efficacy and safety of the PI3K inhibitor buparlisib in combination with tamoxifen in hormone receptor‐positive (HR+), HER2‐negative advanced breast cancer patients after failure of prior endocrine therapy. In this open‐label, single‐arm phase II trial, 25 patients were enrolled in 11 sites in Germany. Patients were stratified according to PIK3CA mutation status (tissue and cfDNA from serum samples) and/or loss of PTEN expression. Patients received buparlisib (100 mg) and tamoxifen (20 mg) once daily on a continuous schedule (28‐day cycle) until progression or unacceptable toxicity.
Association between Use of Angiotensin-converting Enzyme Inhibitors or Angiotensin Receptor Blockers and Postoperative Delirium

Background: Angiotensin-converting enzyme inhibitors and angiotensin receptor blockers improve cognitive function. The authors therefore tested the primary hypothesis that preoperative use of angiotensin inhibitors is associated with less delirium in critical care patients. Post hoc, the association between postoperative use of angiotensin system inhibitors and delirium was assessed. Methods: The authors conducted a single-site cohort study of adults admitted to Cleveland Clinic critical care units after noncardiac procedures between 2013 and 2018 who had at least one Confusion Assessment Method delirium assessment. Patients with preexisting dementia, Alzheimer’s disease or other cognitive decline, and patients who had neurosurgical procedures were excluded. For the primary analysis, the confounder-adjusted association between preoperative angiotensin inhibitor use and the incidence of postoperative delirium was assessed. Post hoc, the confounder-adjusted association between postoperative angiotensin system inhibitor use and the incidence of delirium was assessed. Results: The incidence of delirium was 39% (551 of 1,396) among patients who were treated preoperatively with angiotensin system inhibitors and 39% (1,344 of 3,468) in patients who were not. The adjusted odds ratio of experiencing delirium during critical care was 0.98 (95% CI, 0.86 to 1.10; P = 0.700) for preoperative use of angiotensin system inhibitors versus control. Delirium was observed in 23% (100 of 440) of patients who used angiotensin system inhibitors postoperatively before intensive care discharge, and in 41% (1,795 of 4,424) of patients who did not (unadjusted P < 0.001). The confounder-adjusted odds ratio for experiencing delirium in patients who used angiotensin system inhibitors postoperatively was 0.55 (95% CI, 0.43 to 0.72; P < 0.001). Conclusions: Preoperative use of angiotensin system inhibitors is not associated with reduced postoperative delirium. In contrast, treatment during intensive care was associated with lower odds of delirium. Randomized trials of postoperative angiotensin-converting enzymes inhibitors and angiotensin receptor blockers seem justified. In a single-center cohort study of adults admitted to a surgical intensive care unit, preoperative use of angiotensin-converting enzyme inhibitors or angiotensin receptor blockers was not associated with reduced postoperative delirium. However, rapidly starting angiotensin-converting enzyme inhibitors or angiotensin receptor blockers postoperatively was associated with reduced delirium.
Minor temperature shifts do not affect chromosomal ploidy but cause transcriptomic changes in Leishmania braziliensis promastigotes in vitro

BACKGROUND The leishmaniases are complex neglected diseases caused by protozoan parasites of the genus Leishmania. Leishmania braziliensis is the main etiological agent of cutaneous leishmaniasis in the New World. In recent studies, genomic changes such as chromosome and gene copy number variations (CNVs), as well as transcriptomic changes have been highlighted as mechanisms used by Leishmania species to adapt to stress situations. OBJECTIVES The aim of this study was to determine the effect of short-term minor temperature shifts in the genomic and transcriptomic responses of L. braziliensis promastigotes in vitro. METHODS Growth curves, genome and transcriptome sequencing of L. braziliensis promastigotes were conducted from cultures exposed to three different temperatures (24ºC, 28ºC and 30ºC) compared with the control temperature (26ºC). FINDINGS Our results showed a decrease in L. braziliensis proliferation at 30ºC, with around 3% of the genes showing CNVs at each temperature, and transcriptomic changes in genes encoding amastin surface-like proteins, heat shock proteins and transport proteins, which may indicate a direct response to temperature stress. MAIN CONCLUSIONS This study provides evidence that L. braziliensis promastigotes exhibit a decrease in cell density, and noticeable changes in the transcriptomic profiles. However, there were not perceptible changes at chromosome CNVs and only ~3% of the genes changed their copies in each treatment.
The NASA Reflectance Experiment Laboratory (RELAB) Facility: Past, Present, and Future

Overview: The Reflectance Experiment LABoratory (RELAB) is a NASA-supported multi-user spectroscopy facility that has been housed and operated at Brown University for over 30 years. The goal of RELAB is to provide services to acquire and distribute high quality spectral data to members of the NASA, planetary science, and remote sensing communities. The two major components of RELAB are 1) instrumentation to acquire reflectance and transmission spectra and 2) a publicly available database of all spectral data acuiqred over the history of the lab. Instrumentation for acquisition of new spectral data is available to all NASAfunded researchers on a no-charge basis. Interested investigators, including students, may submit samples to RELAB for measurement. Specific research objectives are funded by individual NASA R&A programs, and investigators that utilize RELAB have been funded by a diversity of programs including (but not limited to) Planetary Geology & Geophysics, Cosmochemistry, Astronomy, Mars Data Analysis, Mars Fundamental Research, Lunar Advanced Science and Exploration Research, Solar Sytstem Workings, Exobiology, and NASA graduate student fellowships. RELAB also supports measurements related to planetary missions, including spectral characterization of flight hardware components. All spectral data are made publicly available within three years of their acquisition date, allowing investigators and graduate students appropriate time to publish their results. The open database continues to be used by numerous members of the planetary science and remote sensing communities both within the U.S. and abroad as a reference for the spectral properties of (primarily geologic) materials.
Photogating-controlled ZnO photodetector response for visible to near-infrared light

In recent years, as a direct wide band gap semiconductor, zinc oxide (ZnO) nanomaterial has attracted a lot of attention. However, the widely investigated ZnO materials are strongly limited in fast-response and broadband photodetectors due to their inherent weaknesses, so an effective structure or mechanism of ZnO nanostructure photodetector is greatly needed. In this work, a photogating-controlled photodetector based on a ZnO nanosheet-HfO2-lightly doped Si architecture is demonstrated. Its performance was significantly improved by the photogating-controlled local field at the Si and HfO2 interfaces compared to the findings in other published works on ZnO. Consequently, the photodetector not only effectively balances the responsivity (as high as 5.6 A W−1) and response time (400 µs), but also broadens the wavelength response of the ZnO-based photodetectors from visible to near-infrared light range (~1200 nm). Additionally, the photogating-controlled ZnO photodetector enables high-resolution imaging both in the visible and near-infrared bands. Our photogating-controlled ZnO photodetectors not only exemplify the controllability of the gate electrode in high mobility materials but also provide a basis for the development of fast speed and high responsivity detection of high mobility materials.
Morpho-agronomic trait comparisons among Tagetes patula L. cultivars

The objective of this work was to characterize Tagetes patula L. cultivars (Spry, Orange, Flame and Yellow) as to the following morpho-agronomic characteristics: plant height, number of stems and inflorescences / plant, stem and inflorescence diameters, flowering cycles and durations, fresh and dry matter weights of aerial parts (including stem, leaves and flowers) and roots The work has been carried out in a greenhouse at the Genetics Department, Campinas Agronomic Institute, Sao Paulo State, Brazil. A randomized complete blocks design was used with four replicates. The results revealed that the late flowering cycle cultivars revealed higher plants and thicker stems, bigger inflorescences, higher dry matter weights in aerial parts and roots and shorter blooming period durations. Early flowering cycle length cultivars presented higher number of inflorescences per stem and longer blooming period durations.
Melatonin-induced phase and dose responses in a diurnal mammal, Funambulus pennantii

ABSTRACT Melatonin, an essential pineal hormone, acts as a marker of the circadian clock that regulates biological rhythms in animals. The effects of exogenous melatonin on the circadian system of nocturnal rodents have been extensively studied; however, there is a paucity of studies on the phase-resetting characteristics of melatonin in diurnal rodents. We studied the phase shifting effects of exogenous melatonin as a single melatonin injection (1 mg/kg) at various phases of the circadian cycle on the circadian locomotor activity rhythm in the palm squirrel, Funambulus pennantii. A phase response curve (PRC) was constructed. Adult male squirrels (N = 10) were entrained to a 12:12 h light-dark cycle (LD) in a climate-controlled chronocubicle with food and water provided ad libitum. After stable entrainment, squirrels were transferred to constant dark condition (DD) for free-running. Following stable free run, animals were administered a single dose of melatonin (1 mg/kg in 2% ethanol-phosphate buffered saline (PBS) solution) or vehicle (2% ethanol-PBS solution) at circadian times (CTs) 3 h apart to evoke phase shifts. The phase shifts elicited at various CTs were plotted to generate the PRC. A dose response curve was generated using four doses (0.5, 1, 2 and 4 mg/kg) administered at the CT of maximum phase advance. Melatonin evoked maximum phase advances at CT0 (1.23 ± 0.28 h) and maximum phase delays at CT15 (0.31 ± 0.09 h). In the dose response experiment, maximal phase shifts were evoked with 1 mg/kg. In contrast, no significant shifts were observed in control groups. Our study demonstrates that the precise timing and appropriate dose of melatonin administration is essential to maximize the amelioration of circadian rhythm–related disorders in a diurnal model.
Scientific evidence and guidelines in occupational medicine

In the past, science has had a conflicting relationship with the philosophy from which it has detached itself due to the scientific method of Galileo Galilei, but anti-scientific attitudes and thoughts still persist in every field of knowledge. Occupational Medicine, like other medical disciplines, increasingly needs to have a scientific foundation that guaran-tees evidence and appropriateness for its varied professional activities. Guidance tools for occupational physicians and, in particular, the Guidelines of Scientific Societies repre-sent an indispensable contribution to correct professional practice. In many countries, in addition to the International Society of Reference and International Commission of Occu-pational Health (ICOH), there are National Societies of Occupational Medicine and many of these, such as the Italian Society of Occupational Medicine, regularly publish policy tools and guidelines for the occupational physician. It is not always possible to base the Guidelines in the field of occupational medicine exclusively on consolidated scientific evidence but it is still necessary to increase research and publications aimed at evaluating the effectiveness of specific interventions in the preventive, clinical and rehabilitative field of occupational medicine in order to guide occupational physicians to an increasingly appropriate practice. In Italy, a recent law allows the production of Guidelines that partially exempt criminal liability for inexperience through a System of Guidelines produced by accredited Scientific Societies.
Intranasal Colonization by Streptococcus Pneumoniae Induces Immunological Protection from Pulmonary and Systemic Infection: A Dissertation

Given that Streptococcus pneumoniae can cause life-threatening pulmonary and systemic infection, an apparent paradox is that the bacterium resides, usually harmlessly, in the nasopharynx of many people. Humoral immunity is thought to be the primary defense against serious pneumococcal infection, and we hypothesized that nasopharyngeal colonization of mice results in the generation of an antibody response that provides long-term protection against lung infection. We found that survival of of C57L/6 mice after intranasal inoculation with wild-type serotype 4 strain TIGR4 pneumococci required B cells but not T cells, suggesting that nasopharyngeal colonization elicited a protective humoral immune response. In fact, intranasal inoculation resulted in detectable pneumococcal-specific antibody responses, and protected mice against a subsequent high-dose S. pneumoniae pulmonary challenge. B cells were required for this response, and transfer of immune sera from i.n. colonized mice, or monoclonal antibodies against phosphorylcholine, a common surface antigen of S. pneumoniae , was sufficient to confer protection. IgA, which is thought to participate in mucosal immunity, contributed to but was not absolutely required for protection from pulmonary challenge. Protection induced by i.n. colonization lasted at least ten weeks. Although it was partially dependent on T cells, depletion of CD4 + T cells at the time of challenge did not alter protection, suggesting that T cells did not provide essential help in activation of conventional memory cells. Peritoneal B1b cells and radiation-resistant, long-lived antibody secreting cells have previously been shown to secrete anti-pneumococcal antibodies and mediate protection against systemic infection following immunization with killed bacteria or capsular polysaccharide [1, 2]. We found that peritoneal cells were not sufficient for colonization-induced protection, but sub-lethally irradiated mice largely survived pulmonary challenge. Thus, our results are consistent with the hypothesis that nasopharyngeal colonization, a common occurrence in humans, is capable of eliciting extended protection against invasive pneumococcal disease by generating long-lived antibody-secreting cells.
Effects of nitrogen deficiency on plant growth, leaf photosynthesis, and hyperspectral reflectance properties in castor (Ricinus communis L.)

Nitrogen affects several processes in plants and accurate detection of plant N status can help farm managers make appropriate N management decisions. An experiment was conducted under outdoor pot-culture conditions to determine the effects of nitrogen deficiency on castor growth, physiology, and leaf hyperspectral reflectance properties. Castor, cv. Hale, was seeded in 12-L pots filled with fine sand and were irrigated with half-strength Hoagland’s nutrient solution from emergence to 34 days after sowing (DAS). Thereafter, the following treatments were initiated: (1) control (100% N) continued receiving the half-strength nutrient solution; (2) reduced N to 20% of the control (20% N); and (3) withheld N from the solution (0% N). Photosynthetic rate, photosynthetic pigments, N concentrations, and hyperspectral reflectance of the uppermost, fully expanded leaves were determined at 3 to 4-day interval from 34 to 64 DAS. Based on stem lengths, leaf numbers and leaf length measurements growth and developmental rates were calculated. At 64 DAS, dry weights of various plant components were measured. Leaf and stem growth rates were more sensitive to leaf N than photosynthesis and leaf addition rates. Among plant dry weight components, leaf dry weight had the greatest and root dry weight had the smallest decrease under N-deficiency. N deficiency stress increased leaf reflectance at 555 (R555) and 715 nm (R715) and caused a rededge shift to shorter wave lengths. Leaf N, chlorophyll and carotenoid contents were correlated with first derivatives of reflectance (dR/dλ) and reflectance ratios. Reflectance ratios, however, enhanced the prediction capabilities of photosynthetic pigments and leaf N content than single wavebands. The N-specific wavebands and the functional relationships between leaf N and growth and developmental processes would be useful for rapid and non-destructive estimation of leaf pigments in castor.