Miracle-dz/UniFAR-FTUs huggingface dataset:
Missing the marine forest for the trees

Seascapes dominated by large, structurally complex seaweeds are ubiquitous. These critical ecosystems are under increasing pressure from human activities, and conceiving successful management strategies to ensure their persistence and/or recovery is of paramount importance. Currently, ecosystems dominated by large seaweeds are referred to as either ‘forests’ or ‘beds’. We demonstrate how this dual terminology is confusing, is used inconsistently, and reduces the efficiency of communication about the importance and perils of seaweed habitats. As a consequence, it undermines work to alleviate and mitigate their loss and impedes research on unifying principles in ecology. We conclude that there are clear benefits of simply using the more intuitive term ‘forest’ to describe all seascapes dominated by habitat-forming seaweeds. This is particularly true as researchers scramble to reconcile ecological functions and patterns of change across disparate regions and species to match the increasingly global scale of environmental forcing on these critical ecosystems.
The Essential Role of Hypermutation in Rapid Adaptation to Antibiotic Stress

A common outcome of antibiotic exposure in patients and in vitro is the evolution of a hypermutator phenotype that enables rapid adaptation by pathogens. While hypermutation is a robust mechanism for rapid adaptation, it requires trade-offs between the adaptive mutations and the more common “hitchhiker” mutations that accumulate from the increased mutation rate. ABSTRACT A common outcome of antibiotic exposure in patients and in vitro is the evolution of a hypermutator phenotype that enables rapid adaptation by pathogens. While hypermutation is a robust mechanism for rapid adaptation, it requires trade-offs between the adaptive mutations and the more common “hitchhiker” mutations that accumulate from the increased mutation rate. Using quantitative experimental evolution, we examined the role of hypermutation in driving the adaptation of Pseudomonas aeruginosa to colistin. Metagenomic deep sequencing revealed 2,657 mutations at ≥5% frequency in 1,197 genes and 761 mutations in 29 endpoint isolates. By combining genomic information, phylogenetic analyses, and statistical tests, we showed that evolutionary trajectories leading to resistance could be reliably discerned. In addition to known alleles such as pmrB, hypermutation allowed identification of additional adaptive alleles with epistatic relationships. Although hypermutation provided a short-term fitness benefit, it was detrimental to overall fitness. Alarmingly, a small fraction of the colistin-adapted population remained colistin susceptible and escaped hypermutation. In a clinical population, such cells could play a role in reestablishing infection upon withdrawal of colistin. We present here a framework for evaluating the complex evolutionary trajectories of hypermutators that applies to both current and emerging pathogen populations.
Blood parameters in fattening pigs from two genetic types fed diet with three different protein concentrations1

Abstract The study aimed to evaluate possible differences between two genetic groups (GG) of pigs, fed diets varying in dietary CP level, in hematological and biochemical plasma profiles. The study was carried out in an experimental farm and involved 36 barrows (average BW 129 ± 11 kg) from two GG: group A (18 Italian Duroc boars × Italian Large White sows) and group D (18 DanBred Duroc), fed three experimental diets: a conventional diet and two low-protein diets (LP1 and LP2). A digestibility/balances trial was carried out on 12 pigs A and 12 pigs D that were housed individually in metabolic cages during four digestibility/balances periods. The experimental design was a factorial design, with 3 diets × 2 GG × 4 periods. The experiment lasted 56 d. Blood was sampled from jugular vein in the morning before feed distribution from all barrows in pens at the start and the end of the experimental period; a supplementary blood sample was collected from the 24 pigs at the end of the four digestibility periods (six pigs per period). Blood was analyzed for hematological and biochemical parameters and serum protein profile using automated analyzers. The GG D showed lower white blood cells (WBC), lymphocyte, and monocyte counts than A group. The GG affected several plasma metabolite concentrations: triglycerides, creatinine, Cl, Fe, alkaline phosphatase, and tartrate-resistant acid phosphatase activities were higher in D groups, while urea, albumin, Ca, Na, total bilirubin, and albumin as percentage of total protein were lower than A group. On the contrary, the dietary protein level neither affects WBC nor their populations; only a trend was reported for erythrocytes (red blood cell) and platelets. The diet affected only plasma urea and total bilirubin concentrations.
Pathogenicity of Aeromonas hydrophila to blunt snout bream Megalobrama amblycephala

This study was carried out to confirm whether Aeromonas hydrophila is a main haemorrhagic pathogen in blunt snout bream Megalobrama amblycephala (BSB). The fish was challenged with bacterial concentrations of 1.7×10 4 , 1.7×10 5 , 1.7×10 6 and 1.7×10 7 cfu/fish for 7 days post infection. The results showed that mortality was bacterial-dose dependent, with 100% mortality observed at 1 day at the highest dose level (1.7×10 7 cfu/fish). For comparison, control fish exhibited cumulative mortalities of 0%. The median lethal dose (LD50) was 5×10 5 cfu/fish. A total of 15 bacterial strains of Aeromonas were re-isolated from challenged fish and re-identified based on morphological characteristics, biochemical tests and genomic DNA gene sequencing. No bacteria were isolated from the control group. This study results indicated that A. hydrophila is capable of causing haemorrhagic septicaemia in BSB. Antibiotic susceptibility test with two strains D4 and HU201301 was investigated; both strains showed sensitive to most of the tested drugs.
Plasmodiale Formiat-Nitrit-Transporter: Biophysikalische Charakterisierung und Entwicklung eines phänotypischen Wirkstoff-Screenings

Malaria stellt mit uber 200 Millionen Fallen im Jahr 2018 eine der schlimmsten Infektionskrankheiten weltweit dar. Von der Malaria tropica, ausgelost durch Plasmodium falciparum, ist vor allem Afrika betroffen. Die vier anderen humanpathogenen Erreger – Plasmodium vivax, Plasmodium knowlesi, Plasmodium ovale und Plasmodium malariae – fuhren im Rest der Welt vermehrt zu Infektionen. Die Behandlung wird durch eine zunehmende Resistenzbildung immer schwieriger. Es ist deshalb wichtig weitere targets fur die Behandlung zu erschliesen. Seit den neunziger Jahren werden dazu Substanzbibliotheken an vielversprechenden targets getestet. Die plasmodialen FNTs sind fur den Abtransport des Stoffwechselendproduktes Laktat zustandig. Wird der FNT gehemmt, stirbt der Malariaerreger ab. Der FNT zeigt sich also als neues target durchaus erfolgsversprechend. Zu Beginn dieser Arbeit waren schon eine Leitstruktur sowie Analoga bekannt. Um das Repertoire zu erweitern und moglichst an einem anderen Teil des Proteins zu wirken, wurde in dieser Arbeit eine phanotypische Screening-Methode entwickelt, mit der viele Substanzen in kurzer Zeit auf ihre Hemmung des FNTs getestet werden konnen. Dieses Screening wurde dabei an der forcierten Resistenzmutante, G107S, fur die bisherige Leitstruktur durchgefuhrt, um eine weitere Bindungsstelle zu identifizieren. Mit dieser Methode wurde die TCAMS-Substanzbibliothek, bestehend aus knapp 13.000 Verbindungen, getestet. Im primaren Screening waren zunachst 92 Substanzen als hits identifiziert worden. Nach Uberprufung in einem biophysikalischen Assay, welcher direkt die Aufnahme von radioaktiv markiertem Laktat messen kann, konnte keiner der hits bestatigt wer-den. Es konnte demnach unter den getesteten 13.000 Substanzen keine gefunden werden, welche den FNT besser hemmt als die bereits bekannte Kontrolle. Des Weiteren wurden die FNT der humanpathogenen Plasmodien miteinander verglichen. Aufgrund ihrer hohen Aminosauren-Sequenzanalogie lag die Vermutung nahe, dass diese Transporter ahnlich transportieren. Wichtiger, dass sie ahnlich gut gehemmt werden konnen. Es wurde dabei gezeigt, dass vor allem der FNT aus P. falciparum und der aus P. malariae in der Transportrate einen signifikanten Unterschied aufweisen. Bei den anderen Proteinen konnte dieser signifikante Unterschied nicht festgestellt werden. Bei der Hemmung bekannter Substanzen konnten Unterschiede im Hemmprofil der Transport-Proteine festgestellt werden.
Identificación molecular de Fusarium spp. aislados de maíz en Sinaloa, México

Fusarium species cause macular diseases in the maize that induce rotting of stems, roots and grains of corn and finally the death of the plant. In the present study, the presence and diversity of Fusarium species associated with these damages in Sinaloa was molecularly identified. During the sowing periods in the years 2013-2014, stem and root tissue from young and adult plants, as well as diseased pod kernels, was collected in the municipalities of Ahome, Culiacan and Elota in the state of Sinaloa. In this investigation, species F. verticillioides, F. oxysporum, F. subglutinans, F. equiseti, F. nygamai, F. cf. bullatum and F. andiyazi, were identified by enzymatic sequencing analysis, where F. verticilloides was the most predominant species. Likewise, the presence in Mexico of Fusarium cf. bullatum causing damage to corn.
A full annual perspective on sex-biased migration timing in long-distance migratory birds

In many taxa, the most common form of sex-biased migration timing is protandry—the earlier arrival of males at breeding areas. Here we test this concept across the annual cycle of long-distance migratory birds. Using more than 350 migration tracks of small-bodied trans-Saharan migrants, we quantify differences in male and female migration schedules and test for proximate determinants of sex-specific timing. In autumn, males started migration about 2 days earlier, but this difference did not carry over to arrival at the non-breeding sites. In spring, males on average departed from the African non-breeding sites about 3 days earlier and reached breeding sites ca 4 days ahead of females. A cross-species comparison revealed large variation in the level of protandry and protogyny across the annual cycle. While we found tight links between individual timing of departure and arrival within each migration season, only for males the timing of spring migration was linked to the timing of previous autumn migration. In conclusion, our results demonstrate that protandry is not exclusively a reproductive strategy but rather occurs year-round and the two main proximate determinants for the magnitude of sex-biased arrival times in autumn and spring are sex-specific differences in departure timing and migration duration.
Maximizing Submodular Functions for Recommendation in the Presence of Biases

Subset selection tasks, arise in recommendation systems and search engines and ask to select a subset of items that maximize the value for the user. The values of subsets often display diminishing returns, and hence, submodular functions have been used to model them. If the inputs defining the submodular function are known, then existing algorithms can be used. In many applications, however, inputs have been observed to have social biases that reduce the utility of the output subset. Hence, interventions to improve the utility are desired. Prior works focus on maximizing linear functions—a special case of submodular functions—and show that fairness constraint-based interventions can not only ensure proportional representation but also achieve near-optimal utility in the presence of biases. We study the maximization of a family of submodular functions that capture functions arising in the aforementioned applications. Our first result is that, unlike linear functions, constraint-based interventions cannot guarantee any constant fraction of the optimal utility for this family of submodular functions. Our second result is an algorithm for submodular maximization. The algorithm provably outputs subsets that have near-optimal utility for this family under mild assumptions and that proportionally represent items from each group. In empirical evaluation, with both synthetic and real-world data, we observe that this algorithm improves the utility of the output subset for this family of submodular functions over baselines.
The dynamics of spawning acts by a semelparous fish and its associated energetic costs

During the reproductive season, animals have to manage both their energetic budget and gamete stock. In particular, for semelparous capital breeders with determinate fecundity and no parental care other than gametic investment, the depletion of energetic stock must match the depletion of gametic stock, so that individuals get exhausted just after their last egg is laid and fertilized. Although these budgets are managed continuously, monitoring the dynamics of mating acts and energy expenditure at a fine temporal scale in the wild is challenging. This study aimed to quantify the individual dynamics of spawning acts and the concomitant energy expenditure of female Allis shad (Alosa alosa) throughout their mating season. Using eight individual-borne accelerometers for one month, we collected tri-axial acceleration, temperature, and pressure data that we analysed to i) detect the timing of spawning acts, ii) estimate energy expenditure from tail beat frequency and water temperature, and iii) monitor changes in body roundness from the position of the dorsally-mounted tag relative to the vertical plane. Female shad had a higher probability to spawn during warmer nights, and their spawning acts were synchronized (both individually and inter-individually) within each active night. They experienced warmer temperature, remained deeper, swan more slowly and spent less energy during daytime than night time. Over one month of spawning, they performed on average 15.75 spawning acts, spent on average 6 277 kJ and died with a significant portion of residual oocytes. The acceleration-based indicator of body roundness was correlated to condition coefficient measured at capture, and globally decreased through the spawning season, although the indicator was noisy and was not correlated to changes in estimated energy expenditure. Despite significant individual variability, our results indicate that female shad exhausted their energetic stock faster than their egg stock. Water warming will increase the rate of energy expenditure, which might increase the risk that shad die with a large stock of unspent eggs. Although perfectible, the three complementary analyses of acceleration data are promising for in situ monitoring of energy expenditure related to specific behaviour.
KAE-Informer: A Knowledge Auto-Embedding Informer for Forecasting Long-Term Workloads of Microservices

Accurately forecasting workloads in terms of throughput that is quantified as queries per second (QPS) is essential for microservices to elastically adjust their resource allocations. However, long-term QPS prediction is challenging in two aspects: 1) generality across various services with different temporal patterns, 2) characterization of intricate QPS sequences which are entangled by multiple components. In this paper, we propose a knowledge auto-embedding Informer network (KAE-Informer) for forecasting the long-term QPS sequences of microservices. By analyzing a large number of microservice traces, we discover that there are two main decomposable and predictable components in QPS sequences, namely global trend & dominant periodicity (TP) and low-frequency residual patterns with long-range dependencies. These two components are important for accurately forecasting long-term QPS. First, KAE-Informer embeds the knowledge of TP components through mathematical modeling. Second, KAE-Informer designs a convolution ProbSparse self-attention mechanism and a multi-layer event discrimination scheme to extract and embed the knowledge of local context awareness and event regression effect implied in residual components, respectively. We conduct experiments based on three real datasets including a QPS dataset collected from 40 microservices. The experiment results show that KAE-Informer achieves a reduction of MAPE, MAE and RMSE by about 16.6%, 17.6% and 23.1% respectively, compared to the state-of-the-art models.
Scan Me If You Can: Understanding and Detecting Unwanted Vulnerability Scanning

Web vulnerability scanners (WVS) are an indispensable tool for penetration testers and developers of web applications, allowing them to identify and fix low-hanging vulnerabilities before they are discovered by attackers. Unfortunately, malicious actors leverage the very same tools to identify and exploit vulnerabilities in third-party websites. Existing research in the WVS space is largely concerned with how many vulnerabilities these tools can discover, as opposed to trying to identify the tools themselves when they are used illicitly. In this work, we design a testbed to characterize web vulnerability scanners using browser-based and network-based fingerprinting techniques. We conduct a measurement study over 12 web vulnerability scanners as well as 159 users who were recruited to interact with the same web applications that were targeted by the evaluated WVSs. By contrasting the traffic and behavior of these two groups, we discover tool-specific and type-specific behaviors in WVSs that are absent from regular users. Based on these observations, we design and build ScannerScope, a machine-learning-based, web vulnerability scanner detection system. ScannerScope consists of a transparent reverse proxy that injects fingerprinting modules on the fly without the assistance (or knowledge) of the protected web applications. Our evaluation results show that ScannerScope can effectively detect WVSs and protect web applications against unwanted vulnerability scanning, with a detection accuracy of over 99% combined with near-zero false positives on human-visitor traffic. Finally, we show that the asynchronous design of ScannerScope results in a negligible impact on server performance and demonstrate that its classifier can resist adversarial ML attacks launched by sophisticated adversaries.
A FACTOR VIII BINDING DOMAIN RESIDES WITHIN THE AMINO-TERMINAL 272 AMINO ACID RESIDUES OF VON WILLEBRAND FACTOR

We have identified a Factor VIII (FVIII) binding domain residing within the amino-terminal 272 amino acid residues of the mature von Willebrand Factor (vWF) subunit. Two dimensional crossed immunoelectrophoresis showed direct binding of purified human FVIII to purified human vWF. After proteolytic digestion of vWF with Staphylococcus aureus V8 protease, FVIII binding was seen only with the amino-terminal SP fragment III and not with the carboxy-terminal SP fragment II. A monoclonal anti-vWF antibody (C3) partially blocked FVIII binding to vWF and SP fragment III. FVIII also bound to vWF which had been adsorbed to polystyrene beads. This binding was inhibited in a dose dependent manner by whole vWF, SP fragment III, and by monoclonal antibody C3. Binding could not be inhibited by SP fragment I, which contains the middle portion of the vWF molecule, or by reduced and alkylated whole vWF. SP fragment II caused only minor inhibition. Trypsin cleavage of SP fragment III produced a 35-kDa fragment containing the amino-terminal 272 amino acid residues of vWF. This fragment reacted with monoclonal antibody C3 and inhibited the binding of FVIII to vWF in a dose dependent manner. The other major fragment obtained from this digestion was a two chain hetero-dimer composed of amino acid residues 273-511 and 674-728. This fragment did not inhibit FVIII binding. These studies demonstrate that a major FVIII binding site resides within the first 272 amino acid residues of vWF.
Osteoporosis genome‐wide association study variant c.3781 C>A is regulated by a novel anti‐osteogenic factor miR‐345‐5p

Upstream transcription factor family member 3 (USF3) c.3781C>A (rs1026364) in the 3′‐untranslated region (3′‐UTR) has been firmly associated with bone mineral density (BMD) in genome‐wide association study (GWAS). However, the molecular mechanism by which it influences BMD and osteoporosis is unknown. Bioinformatics analyses suggested that the risk c.3781A allele creates a target site for hsa‐miR‐345‐5p binding. Luciferase assay validated that the c.3781A allele displayed significantly lower luciferase activities than the c.3781C allele in the human osteoblast cell line hFOB1.19, osteosarcoma cell lines U‐2OS and Saos‐2, and embryonic kidney cell line 293T. Furthermore, hsa‐miR‐345‐5p regulated USF3 expression on both messenger RNA and protein levels in hFOB1.19 and U937 cells with heterozygous A/C genotype. Transfection of hsa‐miR‐345‐5p antagomiR in heterozygous hFOB1.19 cells significantly increased the expression of osteogenic marker genes RUNX2, OSTERIX, COL1A1, ALP, OPN, OCN, and alkaline phosphatase activity and matrix mineralization level. Importantly, we found that hsa‐miR‐345‐5p also inhibits osteoblast maturation in cell lines U‐2OS with hsa‐miR‐345‐5p nonbinding C/C genotype by targeting RUNX3 and SMAD1. Our findings uncovered a novel pathogenetic mechanism of osteoporosis by GWAS variant c.3781C>A‐mediated disruption of hsa‐miR‐345‐5p binding at the 3′‐UTR of USF3 and the functional role of hsa‐miR‐345‐5p in osteogenic differentiation.
Out of the Lab, Into the Frying Pan: Understanding the Effect of Natural Groundwater Conditions on Bio-Based Ground Improvement Strategies

<p>We are developing a biogeochemical model for microbial denitrification-driven ground improvement to account for t the complexities expected in the field, including microbial inhibition and competition. We will use this model to support Microbially Induced Desaturation and Precipitation (MIDP) via denitrification as a bio-based ground improvement strategy alternative considering different treatment recipes and natural groundwater composition. Current ground improvement techniques have limited utility underneath or near existing structures. Developing alternatives is becoming increasingly important as urbanization increases. Large, centralized populations and infrastructure are more vulnerable to threats by natural disasters and geologic hazards such as earthquake-induced liquefaction and flooding. Bio-based ground stabilization techniques may be less disruptive to deploy and monitor, allowing application underneath existing structures. MIDP is a two-stage ground-improvement process in which biogenic gas desaturation provides immediate improvement while calcium carbonate precipitation provides long term stability. MIDP influences the geochemical environment and the hydro-mechanical behavior of soils through biogenic gas production, precipitation of calcium carbonate, and biomass growth. All three components alter the biogeochemical environment and subsurface permeability, thereby affecting the transport of substrates and subsequent product formation. The products of MIDP mitigate liquefaction at the lab-scale. MIDP experimentation and modeling have primarily considered only the use of de-ionized water and simplified water composition. However, denitrifying microorganisms compete with alternative electron acceptors, like sulfate and iron, and are influenced by the environment&#8217;s pH and salinity which may impede the MIDP treatment. Our biogeochemical model can predict the products and by-products of MIDP treatment considering realistic groundwater conditions. The results of this model will be used to develop comprehensive treatment plans for upcoming field trials to demonstrate treatment effectiveness and develop best practices for future application. </p>