Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Lactic Acid Bacteria Phospho-β-Glucosidases during the Fermentation of Cereal by-Products

Bioprocessing using lactic acid bacteria (LAB) is a powerful means to exploit plant-derived by-products as a food ingredient. LAB have the capability to metabolize a large variety of carbohydrates, but such metabolism only relies on few metabolic routes, conferring on them a high fermentation potential. One example of these pathways is that involving phospho-β-glucosidase genes, which are present in high redundancy within LAB genomes. This enzymatic activity undertakes an ambivalent role during fermentation of plant-based foods related to the release of a wide range of phenolic compounds, from their β-D-glycosylated precursors and the degradation of β-glucopyranosyl derived carbohydrates. We proposed a novel phenomic approach to characterize the metabolism drift of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides caused by a lignocellulosic by-product, such as the brewers’ spent grain (BSG), in contrast to Rich De Man, Rogosa and Sharpe (MRS) broth. We observed an increased metabolic activity for gentiobiose, cellobiose and β-glucoside conjugates of phenolic compounds during BSG fermentation. Gene expression analysis confirmed the importance of cellobiose metabolism while a release of lignin-derived aglycones was found during BSG fermentation. We provided a comprehensive view of the important role exerted by LAB 6-phospho-β-glucosidases as well the major metabolic routes undertaken during plant-based fermentations. Further challenges will consider a controlled characterization of pbg gene expression correlated to the metabolism of β-glucosides with different aglycone moieties.
A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies

Plants and insects often use the same compounds for chemical communication, but not much is known about the genetics of convergent evolution of chemical signals. The terpene (E)-β-ocimene is a common component of floral scent and is also used by the butterfly Heliconius melpomene as an anti-aphrodisiac pheromone. While the biosynthesis of terpenes has been described in plants and microorganisms, few terpene synthases (TPSs) have been identified in insects. Here, we study the recent divergence of 2 species, H. melpomene and Heliconius cydno, which differ in the presence of (E)-β-ocimene; combining linkage mapping, gene expression, and functional analyses, we identify 2 novel TPSs. Furthermore, we demonstrate that one, HmelOS, is able to synthesise (E)-β-ocimene in vitro. We find no evidence for TPS activity in HcydOS (HmelOS ortholog of H. cydno), suggesting that the loss of (E)-β-ocimene in this species is the result of coding, not regulatory, differences. The TPS enzymes we discovered are unrelated to previously described plant and insect TPSs, demonstrating that chemical convergence has independent evolutionary origins.
The joint dynamics of investor beliefs and trading during the COVID-19 crash

Significance We analyze how investor expectations about economic growth and stock returns changed during the February−March 2020 stock market crash induced by the COVID-19 pandemic, as well as during the subsequent partial stock market recovery. Our results provide guidance for the design of macro and finance models and related economic policies. We analyze how investor expectations about economic growth and stock returns changed during the February−March 2020 stock market crash induced by the COVID-19 pandemic, as well as during the subsequent partial stock market recovery. We surveyed retail investors who are clients of Vanguard at three points in time: 1) on February 11–12, around the all-time stock market high, 2) on March 11–12, after the stock market had collapsed by over 20%, and 3) on April 16–17, after the market had rallied 25% from its lowest point. Following the crash, the average investor turned more pessimistic about the short-run performance of both the stock market and the real economy. Investors also perceived higher probabilities of both further extreme stock market declines and large declines in short-run real economic activity. In contrast, investor expectations about long-run (10-y) economic and stock market outcomes remained largely unchanged, and, if anything, improved. Disagreement among investors about economic and stock market outcomes also increased substantially following the stock market crash, with the disagreement persisting through the partial market recovery. Those respondents who were the most optimistic in February saw the largest decline in expectations and sold the most equity. Those respondents who were the most pessimistic in February largely left their portfolios unchanged during and after the crash.
Using Piezoresistance Model With $C$– $R$ Conversion for Modeling of Strain-Induced Mobility

The piezoresistance model has commonly been used to describe mobility enhancement for low levels of process induced strain in CMOS technology. However, many reports show it failing to describe the superlinear behavior observed at high levels of stress. This is because the approximation made is only valid for very low stress levels. In this letter, a conversion between the change in conductivity and resistivity is developed such that a piezoresistance model can be applied correctly to calculate the strain-induced mobility changes. Hence, the overall accuracy is improved compared to the conventional formulation. Its significance is confirmed with the results from Monte Carlo simulations of mobility, nMOSFETs, pMOSFETs, and nanowires.
Obesogenic home food availability, diet, and BMI in Pakistani and White toddlers

Abstract Individuals of South Asian ethnicity have an increased risk for obesity and related diseases. Foods available in the home during the first 1000 days (conception to 24 months old) are an important determinant of diet, yet no study has examined the association of early‐life home food availability (HFA) with later diet and obesity risk in South Asian households. We examined whether obesogenic HFA at 18 months of age is associated with dietary intake and body mass index (BMI) at 36 months of age in low‐income Pakistani and White households in the United Kingdom. In this prospective birth cohort study (Born in Bradford 1000), follow‐up assessments occurred at 18 (n = 1032) and 36 (n = 986) months of age. Variety and quantity of snack foods and sugar‐sweetened beverages (SSBs) in the home and consumed were measured using the HFA Inventory Checklist and food frequency questionnaires, respectively. BMI was calculated using measured length/height and weight. Multinomial logistic regression models examined associations between HFA and tertiles of dietary intake, and multivariable linear regression models assessed associations between HFA and BMI. Pakistani households had a greater variety and quantity of snack foods and SSBs available compared with White households. Variety and quantity of snack foods and SSBs in the home at 18 months were positively associated with children's intake of these items at 36 months, but associations between HFA and BMI were null. Reducing obesogenic HFA during the first 1000 days may promote the development of more healthful diets, though this may not be associated with lower obesity risk during toddlerhood.
Risk of 28-day readmissions among stroke patients in Malaysia (2008–2015): Trends, causes and its associated factors

Background and objectives Risk of readmissions is an important quality indicator for stroke care. Such information is limited among low- and middle-income countries. We assessed the trends for 28-day readmissions after a stroke in Malaysia from 2008 to 2015 and evaluated the causes and factors associated with readmissions in 2015. Methods Using the national hospital admission records database, we included all stroke patients who were discharged alive between 2008 and 2015 for this secondary data analysis. The risk of readmissions was described in proportion and trends. Reasons were coded according to the International Classification of Diseases, 10th Edition. Multivariable logistic regression was performed to identify factors associated with readmissions. Results Among 151729 patients, 11 to 13% were readmitted within 28 days post-discharge from their stroke events each year. The trend was constant for ischemic stroke but decreasing for hemorrhagic stroke. The leading causes for readmissions were recurrent stroke (32.1%), pneumonia (13.0%) and sepsis (4.8%). The risk of 28-day readmission was higher among those with stroke of hemorrhagic (adjusted odds ratio (AOR): 1.52) and subarachnoid hemorrhage (AOR: 2.56) subtypes, and length of index admission >3 days (AOR: 1.48), but lower among younger age groups of 35–64 (AORs: 0.61–0.75), p values <0.001. Conclusion The risk of 28-day readmission remained constant from 2008 to 2015, where one in eight stroke patients required readmission, mainly attributable to preventable causes. Age, ethnicity, stroke subtypes and duration of the index admission influenced the risk of readmission. Efforts should focus on minimizing potentially preventable admissions, especially among those at higher risk.
An unusual cause of visual loss: Subfoveal, motile angiostrongyliasis

This is a short report describing the clinical presentation, investigations, treatment and outcome of a patient living in the Jamaican countryside who was diagnosed with a live, motile subfoveal helminth identified as Angiostrongylus cantonensis on optical coherence tomography at the University Hospital of the West Indies Eye Clinic. This is the second documented case in Jamaica. Early recognition of angiostrongyliasis is important as it may manifest as eosinophilic meningitis which can be fatal without prompt treatment.
Two Metabolomics Phenotypes of Human Hepatocellular Carcinoma in Non-Alcoholic Fatty Liver Disease According to Fibrosis Severity

Non-Alcoholic Fatty Liver Disease (NAFLD) is considered as the forthcoming predominant cause for hepatocellular carcinoma (HCC). NAFLD-HCC may rise in non-cirrhotic livers in 40 to 50% of patients. The aim of this study was to identify different metabolic pathways of HCC according to fibrosis level (F0F1 vs. F3F4). A non-targeted metabolomics strategy was applied. We analyzed 52 pairs of human HCC and adjacent non-tumoral tissues which included 26 HCC developed in severe fibrosis or cirrhosis (F3F4) and 26 in no or mild fibrosis (F0F1). Tissue extracts were analyzed using 1H-Nuclear Magnetic Resonance spectroscopy. An optimization evolutionary method based on genetic algorithm was used to identify discriminant metabolites. We identified 34 metabolites differentiating the two groups of NAFLD-HCC according to fibrosis level, allowing us to propose two metabolomics phenotypes of NAFLD-HCC. We showed that HCC-F0F1 mainly overexpressed choline derivatives and glutamine, whereas HCC-F3F4 were characterized by a decreased content of monounsaturated fatty acids (FA), an increase of saturated FA and an accumulation of branched amino acids. Comparing HCC-F0F1 and HCC-F3F4, differential expression levels of glucose, choline derivatives and phosphoethanolamine, monounsaturated FA, triacylglycerides were identified as specific signatures. Our metabolomics analysis of HCC tissues revealed for the first time two phenotypes of HCC developed in NAFLD according to fibrosis level. This study highlighted the impact of the underlying liver disease on metabolic reprogramming of the tumor.
Titanium Dioxide Presents a Different Profile in Dextran Sodium Sulphate-Induced Experimental Colitis in Mice Lacking the IBD Risk Gene Ptpn2 in Myeloid Cells

Environmental and genetic factors have been demonstrated to contribute to the development of inflammatory bowel disease (IBD). Recent studies suggested that the food additive; titanium dioxide (TiO2) might play a causative role in the disease. Therefore, in the present study we aimed to explore the interaction between the food additive TiO2 and the well-characterized IBD risk gene protein tyrosine phosphatase non-receptor type 2 (Ptpn2) and their role in the development of intestinal inflammation. Dextran sodium sulphate (DSS)-induced acute colitis was performed in mice lacking the expression of Ptpn2 in myeloid cells (Ptpn2LysMCre) or their wild type littermates (Ptpn2fl/fl) and exposed to the microparticle TiO2. The impact of Ptpn2 on TiO2 signalling pathways and TiO2-induced IL-1β and IL-10 levels were studied using bone marrow-derived macrophages (BMDMs). Ptpn2LysMCre exposed to TiO2 exhibited more severe intestinal inflammation than their wild type counterparts. This effect was likely due to the impact of TiO2 on the differentiation of intestinal macrophages, suppressing the number of anti-inflammatory macrophages in Ptpn2 deficient mice. Moreover, we also found that TiO2 was able to induce the secretion of IL-1β via mitogen-activated proteins kinases (MAPKs) and to repress the expression of IL-10 in bone marrow-derived macrophages via MAPK-independent pathways. This is the first evidence of the cooperation between the genetic risk factor Ptpn2 and the environmental factor TiO2 in the regulation of intestinal inflammation. The results presented here suggest that the ingestion of certain industrial compounds should be taken into account, especially in individuals with increased genetic risk
Consequences of adaptation of TAL effectors on host susceptibility to Xanthomonas

Transcription activator-like effectors (TALEs) are virulence factors of Xanthomonas that induce the expression of host susceptibility (S) genes by specifically binding to effector binding elements (EBEs) in their promoter regions. The DNA binding specificity of TALEs is dictated by their tandem repeat regions, which are highly variable between different TALEs. Mutation of the EBEs of S genes is being utilized as a key strategy to generate resistant crops against TALE-dependent pathogens. However, TALE adaptations through rearrangement of their repeat regions is a potential obstacle for successful implementation of this strategy. We investigated the consequences of TALE adaptations in the citrus pathogen Xanthomonas citri subsp. citri (Xcc), in which PthA4 is the TALE required for pathogenicity, whereas CsLOB1 is the corresponding susceptibility gene, on host resistance. Seven TALEs, containing two-to-nine mismatching-repeats to the EBEPthA4 that were unable to induce CsLOB1 expression, were introduced into Xcc pthA4:Tn5 and adaptation was simulated by repeated inoculations into and isolations from sweet orange for a duration of 30 cycles. While initially all strains failed to promote disease, symptoms started to appear between 9–28 passages in four TALEs, which originally harbored two-to-five mismatches. Sequence analysis of adapted TALEs identified deletions and mutations within the TALE repeat regions which enhanced putative affinity to the CsLOB1 promoter. Sequence analyses suggest that TALEs adaptations result from recombinations between repeats of the TALEs. Reintroduction of these adapted TALEs into Xcc pthA4:Tn5 restored the ability to induce the expression of CsLOB1, promote disease symptoms and colonize host plants. TALEs harboring seven-to-nine mismatches were unable to adapt to overcome the incompatible interaction. Our study experimentally documented TALE adaptations to incompatible EBE and provided strategic guidance for generation of disease resistant crops against TALE-dependent pathogens.
The Synthesis and Characterisation of Bis(phosphane)‐Linked (6‐p‐Cymene)ruthenium(II)–Borane Compounds

The reaction of [(η6-p-cymene)RuCl2]2 with some bis(phosphane) ligands (dppm, dppe, dppv, dppa, dpp14b, dppf) has been investigated. In general mixtures of products were obtained, although the pendant phosphane complexes [(η6-p-cymene)RuCl2(η1-dppv)] and [(η6-p-cymene)RuCl2(η1-dppa)] were isolated and characterized in the solid state by X-ray diffraction. The later complex was obtained in lower yield and undergoes an equilibration reaction resulting in the formation of a dimeric species, where the dppa bridges two ruthenium centres, and uncoordinated phosphane; the bridging species was also structurally characterised in the solid state. In contrast, the reaction of [(η6-p-cymene)RuCl2(PPh3)] with dppa in the presence of [NH4]PF6 results in the formation of [(η6-p-cymene)RuCl(PPh3)(η1-dppa)]PF6, which is stable in solution. A series of linked ruthenium-borane complexes, viz. [(η6-p-cymene)RuCl2(η1-phosphane-BH3)] (phosphane = dppm, dppe, dppv, dppa, dpp14b, dppf) and [(η6-p-cymene)RuCl(PPh3)(η1-dppa-BH3)]PF6 have been prepared from isolated pendant phosphane complexes, those generated in situ, or from a preformed phosphane-borane adduct. The solid-state structures of [(η6-p-cymene)RuCl2(η1-dppm-BH3)], [(η6-p-cymene)RuCl2(η1-dppe-BH3)] and [(η6-p-Cymene)RuCl2(η1-dppv-BH3)] have been determined by X-ray diffraction analysis.
Evaluating the scientific impact of research infrastructures: The role of current research information systems

Research infrastructures (RIs) offer researchers a multitude of research opportunities and services and play a key role in the performance, innovative strength, and international competitiveness of science. As an important part of the generation and use of new knowledge and technologies, they are essential for research policies. Because of their strategic importance and their need for significant funding, there is a growing demand for the assessment of their scientific output and impact. Current research information systems (CRIS) have contributed for many years now to the evaluation of universities and research organizations. Based on studies on the application of CRIS to infrastructures and on a recent French report on the scientometric assessment of RI, this paper analyzes the potential of CRIS and their data models and standards (in particular the international CERIF format and the German RDC model) for the monitoring and evaluation of RIs. The interaction between functional specificities of RI and standards for their assessment is outlined, with reference to their own potential to stimulate and share innovation in the networks located inside and outside RIs. This societal challenge, more than an academic issue, is on the way to further harmonization and consolidation of shared and common RI metrics.
Lutsig: a verified Verilog compiler for verified circuit development

We report on a new verified Verilog compiler called Lutsig. Lutsig currently targets (a class of) FPGAs and is capable of producing technology mapped netlists for FPGAs. We have connected Lutsig to existing Verilog development tools, and in this paper we show how Lutsig, as a consequence of this connection, fits into a hardware development methodology for verified circuits in the HOL4 theorem prover. One important step in the methodology is transporting properties proved at the behavioral Verilog level down to technology mapped netlists, and Lutsig is the component in the methodology that enables such transportation.
Can Replay Attacks Designed to Steal Water from Water Distribution Systems Remain Undetected?

Industrial Control Systems (ICS) monitor and control physical processes. ICS are found in, among others, critical infrastructures such as water treatment plants, water distribution systems, and the electric power grid. While the existence of cyber-components in an ICS leads to ease of operations and maintenance, it renders the system under control vulnerable to cyber and physical attacks. An experimental study was conducted with replay attacks launched on an operational water distribution (WADI) plant to understand under what conditions an attacker/attack can remain undetected while stealing water. A detection method, based on an input-output Linear Time-invariant system model of the physical process, was developed and implemented in WADI to detect such attacks. The experiments reveal the strengths and limitations of the detection method and challenges faced by an attacker while attempting to steal water from a water distribution system.
Decentralized Firmware Attestation for In-Vehicle Networks

Today’s vehicles are examples of Cyber-Physical Systems (CPS) controlled by a large number of electronic control units (ECUs), which manage everything from heating to steering and braking. Due to the increasing complexity and inter-dependency of these units, it has become essential for an ECU to be able to ensure the integrity of the firmware running on other ECU’s to guarantee its own correct operation. Existing solutions for firmware attestation use a centralized approach, which means a single point of failure. In this article, we propose and investigate a decentralized firmware attestation scheme for the automotive domain. The basic idea of this scheme is that each ECU can attest to the state of those ECU’s on which it depends. Two flavors of ECU attestation, i.e., parallel and serial solution, were designed, implemented, and evaluated. The two variants were compared in terms of both detection performance (i.e., the ability to identify unauthorized firmware modifications) and timing performance. Our results show that the proposed scheme is feasible to implement and that the parallel solution showed a significant improvement in timing performance over the serial solution.
Fragment growing exploiting dynamic combinatorial chemistry of inhibitors of the aspartic protease endothiapepsin

Fragment-based drug design (FBDD) has emerged as an efficient hit-identification and/or -optimization strategy with a higher hit rate than high-throughput screening (HTS). Whereas fragment linking is more challenging, fragment growing has become the preferred fragment-optimization strategy, requiring synthesis of derivatives and validation of their binding mode at each step of the optimization cycle. Dynamic combinatorial chemistry (DCC) is a powerful and efficient strategy to identify ligands for biological targets. Here, we have demonstrated that the novel combination of fragment-growing and DCC is a highly powerful strategy to grow a fragment into a more potent, non-covalent inhibitor of the aspartic protease endothiapepsin. We have designed a library of acylhydrazones using fragment growing starting from a known fragment in complex with endothiapepsin. We have used DCC and a fluorescence-based enzymatic assay to identify the best hit(s) from the dynamic combinatorial libraries, displaying double-digit micromolar inhibition of endothiapepsin. In addition, each DCC experiment requires only very small amounts of protein compared with established methods of analysis and the protein needs to be in the assay mixture only for a short period of time, making this protocol ideal for precious and unstable proteins. These results constitute a proof of concept that the combination of fragment growing and DCC is a powerful and efficient strategy to convert a fragment into a hit.