Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of Sustainable and Biodegradable Polymers from Agricultural Waste

Agro-wastes are derived from diverse sources including grape pomace, tomato pomace, pineapple, orange, and lemon peels, sugarcane bagasse, rice husks, wheat straw, and palm oil fibers, among other affordable and commonly available materials. The carbon-rich precursors are used in the production bio-based polymers through microbial, biopolymer blending, and chemical methods. The Food and Agriculture Organization (FAO) estimates that 20–30% of fruits and vegetables are discarded as waste during post-harvest handling. The development of bio-based polymers is essential, considering the scale of global environmental pollution that is directly linked to the production of synthetic plastics such as polypropylene (PP) and polyethylene (PET). Globally, 400 million tons of synthetic plastics are produced each year, and less than 9% are recycled. The optical, mechanical, and chemical properties such as ultraviolet (UV) absorbance, tensile strength, and water permeability are influenced by the synthetic route. The production of bio-based polymers from renewable sources and microbial synthesis are scalable, facile, and pose a minimal impact on the environment compared to chemical synthesis methods that rely on alkali and acid treatment or co-polymer blending. Despite the development of advanced synthetic methods and the application of biofilms in smart/intelligent food packaging, construction, exclusion nets, and medicine, commercial production is limited by cost, the economics of production, useful life, and biodegradation concerns, and the availability of adequate agro-wastes. New and cost-effective production techniques are critical to facilitate the commercial production of bio-based polymers and the replacement of synthetic polymers.
Calcium oxalate crystal macropattern development during Prunus virginiana (Rosaceae) leaf growth

In this first study of foliar crystal macropattern initiation and development, primordia to just-shed bud scales, stipules, and leaves were bleached, cleared, and viewed microscopically. Apical clusters of prismatics appear first in the 0.1-mm stipule; crystals proliferate basipetally as stipules elongate. Apical prismatics appear next in a 0.5-mm leaf; they remain isolated until tiny prismatics appear in scattered palisade cells throughout the lamina of a 1.0- to 1.5-cm leaf. Meanwhile, druses proliferate from stem through elongating petioles, reaching the base of 2- to 4-cm leaves. Lamina prismatics enlarge, and new ones appear. In the midvein, short files of tiny druses reach the apex of the 4- to 5-cm leaf, and files of druses extend into lower main lateral veins. In 9- to 11-cm (full-grown) mid-May leaves, lamina prismatics are numerous and conspicuous, but small druses have extended into smaller veins. Until leaf shedding, some lamina prismatics continue to enlarge, new ones form, and others become surrounded by tiny pris- matics. Druses gradually occupy all vein orders, and many in the smallest veins become quite large with conspicuous cores. The mature crystal macropattern shows druses confined to stem, petiole, and leaf veins, whereas prismatics are localized in stipules, bud scales, and leaf lamina.
NMR resonance assignment and structure prediction of the C-terminal domain of the microtubule end-binding protein 3

End-binding proteins (EBs) associate with the growing microtubule plus ends to regulate microtubule dynamics as well as the interaction with intracellular structures. EB3 contributes to pathological vascular leakage through interacting with the inositol 1,4,5-trisphosphate receptor 3 (IP3R3), a calcium channel located at the endoplasmic reticulum membrane. The C-terminal domain of EB3 (residues 200–281) is functionally important for this interaction because it contains the effector binding sites, a prerequisite for EB3 activity and specificity. Structural data for this domain is limited. Here, we report the backbone chemical shift assignments for the human EB3 C-terminal domain and computationally explore its EB3 conformations. Backbone assignments, along with computational models, will allow future investigation of EB3 structural dynamics, interactions with effectors, and will facilitate the development of novel EB3 inhibitors.
Peer support groups after acquired brain injury: a systematic review

ABSTRACT Background Peer support groups can be a way to obtain support, problem solve, and widen social networks. However, there has been no systematic literature review examining the evidence for the use of peer support groups after an acquired brain injury (ABI). Objective This review sought to systematically evaluate the evidence for (1) the psychosocial effectiveness, and (2) the experience of peer support groups in adults who had experienced ABI’s. Methods The systematic literature search was conducted across the following four databases: PsycINFO, PsycARTICLES, MEDLINE, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) in October 2019. The mixed methods appraisal tool was used to examine the quality of the research. Results 13 papers were included in this review. Limited evidence was found for the psychosocial effectiveness of peer support groups in ABI, although the experience of partaking in a peer support group was largely found to be positive. The benefits and helping factors of taking part in a peer support group can be summarized as: being connected, interacting with others, and providing and receiving support. Conclusions The findings of this review suggest that peer support groups could be a promising intervention to support individuals and promote adjustment following an ABI.
Quantifying streams of thought during cognitive task performance using sequence analysis

Streams of thought vary in content from one moment to the next, and these temporal patterns have been argued to be critical to understanding the wandering mind. But few analytic methods have been proposed that can account for both the content and temporal ordering of categorical experience sampling thought probes over time. In the present study, I apply sequence analytic methods to quantify the dynamics of thought from time series sequences of categorical experience sampling thought probes delivered across five different cognitive tasks in the same individuals ( N = 545). Analyses revealed some patterns of consistency in streams of thought within individuals, but also demonstrated considerable variability within and between task sessions. Hierarchical clustering of sequence dissimilarities further revealed common typologies of mind wandering across individuals. These findings demonstrate the application of sequence analytic methods for quantifying the dynamics of thought over the course of task performance and show that contextual task constraints are associated with how streams of thought unfold over time. More broadly, sequence analysis provides a valuable framework for investigation of time ordered cognitive and behavioral processes across psychological domains.
Hypoxia regulates human mast cell adhesion to fibronectin via the PI3K/AKT signaling pathway

ABSTRACT A decrease in oxygen concentration is a hallmark of inflammatory reactions resulting from infection or homeostasis disorders. Mast cells interact with extracellular matrix and other cells by adhesion receptors. We investigated the effect of hypoxia on integrin-mediated mast cell adhesion to fibronectin. We found that it was mediated by the α5/β1 receptor and that hypoxia significantly upregulated this process. Hypoxia-mediated increases in mast cell adhesion occurred without increased surface expression of integrins, suggesting regulation by inside-out integrin signaling. Hypoxia also mediated an increase in phosphorylation of Akt, and PI3’kinase inhibitors abolished hypoxia-mediated mast cell adhesion. Hypoxia upregulates the function of integrin receptors by PI3’ kinase-dependent signaling. This process might be important for the location of mast cells at inflammatory sites
The Chromodorididae (Opisthobranchia: Mollusca) of the Indo-West Pacific: Chromodoris splendida, C. aspersa and Hypselodoris placida colour groups

Eleven species of Chromodoris, two species of Hypselodoris, three species of Mexichromis and one species of Noumea are described from the Indo-West Pacific, of which four species of Chromodoris and one of Mexichromis are new species. All species have a colour pattern dominated by red, purple or black spots. All previously described species with similar colour patterns, from both the Indo-West Pacific and other regions, are discussed.
PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features

Statistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments. PolySTest provides a user-friendly web service for statistical testing, data browsing and visualization, including a new method that simultaneously tests for missingness and feature abundance, thereby complementing common statistical tests by rescuing otherwise discarded data features. By combining different statistical tests, PolySTest improves robustness and confidence for simulated, experimental ground truth, and biological data. Graphical Abstract Highlights Novel statistical test combining missingness and quantitative profiles. Unification of different statistical tests into a PolySTest FDR provides higher robustness and confidence. PolySTest provides higher coverage of relevant biological pathways. User-friendly interactive web service for statistical analysis and visualization. Statistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass spectrometry. Statistical tests need to be sufficiently robust to deal with experiment intrinsic data structures and variations and often also reduced feature coverage across different biological samples due to ubiquitous missing values. A robust statistical test provides accurate confidence scores of large-scale proteomics results, regardless of instrument platform, experimental protocol and software tools. However, the multitude of different combinations of experimental strategies, mass spectrometry techniques and informatics methods complicate the decision of choosing appropriate statistical approaches. We address this challenge by introducing PolySTest, a user-friendly web service for statistical testing, data browsing and data visualization. We introduce a new method, Miss test, that simultaneously tests for missingness and feature abundance, thereby complementing common statistical tests by rescuing otherwise discarded data features. We demonstrate that PolySTest with integrated Miss test achieves higher confidence and higher sensitivity for artificial and experimental proteomics data sets with known ground truth. Application of PolySTest to mass spectrometry based large-scale proteomics data obtained from differentiating muscle cells resulted in the rescue of 10–20% additional proteins in the identified molecular networks relevant to muscle differentiation. We conclude that PolySTest is a valuable addition to existing tools and instrument enhancements that improve coverage and depth of large-scale proteomics experiments. A fully functional demo version of PolySTest and Miss test is available via http://computproteomics.bmb. sdu.dk/Apps/PolySTest.
Genetic structure of Japanese introduced populations of the Golden Mussel, Limnoperna fortunei, and the estimation of their range expansion process

Abstract Limnoperna fortunei (golden mussel) is an aggressive freshwater invasive species naturally distributed in China, Korea, and South eastern Asian countries. This species was introduced into East Asian and South American countries from 1965 to the 1990s. In Japan, the golden mussel was first found in Lake Biwa in 1992 and it is known to be distributed in 10 of 47 prefectures of Japan. We surveyed genetic structures of introduced populations to trace the process of their range expansion in Japan using mitochondrial DNA. Genetic analyses revealed that most Japanese populations show high genetic diversity and include several haplotypes in each population. Although most Japanese populations showed similar genetic structures and shared several haplotypes with each other, populations from the lowland Kanto district showed unique genetic structure. From these results, we considered that invasions of this mussel into Japan from foreign countries had occurred at least twice independently and that several Japanese populations were established by dispersal of individuals from other Japanese populations.
Online National Health Agency Mask Guidance for the Public in Light of COVID-19: Content Analysis

Background The rapid global spread of the coronavirus disease (COVID-19) has compelled national governments to issue guidance on the use of face masks for members of the general public. To date, no work has assessed how this guidance differs across governments. Objective This study seeks to contribute to a rational and consistent global response to infectious disease by determining how guidelines differ across nations and regions. Methods A content analysis of health agency mask guidelines on agency websites was performed in late March 2020 among 25 countries and regions with large numbers of COVID-19 cases. Countries and regions were assigned across the coding team by language proficiency, with Google Translate used as needed. When available, both the original and English language version of guidance were reviewed. Results All examined countries and regions had some form of guidance online, although detail and clarity differed. Although 9 countries and regions recommended surgical, medical, or unspecified masks in public and poorly ventilated places, 16 recommended against people wearing masks in public. There were 2 countries that explicitly recommended against fabric masks. In addition, 12 failed to outline the minimum basic World Health Organization guidance for masks. Conclusions Online guidelines for face mask use to prevent COVID-19 in the general public are currently inconsistent across nations and regions, and have been changing often. Efforts to create greater standardization and clarity should be explored in light of the status of COVID-19 as a global pandemic.
Association of dairy consumption with metabolic syndrome, hypertension and diabetes in 147 812 individuals from 21 countries

Objective Our aims were to assess the association of dairy intake with prevalence of metabolic syndrome (MetS) (cross-sectionally) and with incident hypertension and incident diabetes (prospectively) in a large multinational cohort study. Methods The Prospective Urban Rural Epidemiology (PURE) study is a prospective epidemiological study of individuals aged 35 and 70 years from 21 countries on five continents, with a median follow-up of 9.1 years. In the cross-sectional analyses, we assessed the association of dairy intake with prevalent MetS and its components among individuals with information on the five MetS components (n=112 922). For the prospective analyses, we examined the association of dairy with incident hypertension (in 57 547 individuals free of hypertension) and diabetes (in 131 481 individuals free of diabetes). Results In cross-sectional analysis, higher intake of total dairy (at least two servings/day compared with zero intake; OR 0.76, 95% CI 0.71 to 0.80, p-trend<0.0001) was associated with a lower prevalence of MetS after multivariable adjustment. Higher intakes of whole fat dairy consumed alone (OR 0.72, 95% CI 0.66 to 0.78, p-trend<0.0001), or consumed jointly with low fat dairy (OR 0.89, 95% CI 0.80 to 0.98, p-trend=0.0005), were associated with a lower MetS prevalence. Low fat dairy consumed alone was not associated with MetS (OR 1.03, 95% CI 0.77 to 1.38, p-trend=0.13). In prospective analysis, 13 640 people with incident hypertension and 5351 people with incident diabetes were recorded. Higher intake of total dairy (at least two servings/day vs zero serving/day) was associated with a lower incidence of hypertension (HR 0.89, 95% CI 0.82 to 0.97, p-trend=0.02) and diabetes (HR 0.88, 95% CI 0.76 to 1.02, p-trend=0.01). Directionally similar associations were found for whole fat dairy versus each outcome. Conclusions Higher intake of whole fat (but not low fat) dairy was associated with a lower prevalence of MetS and most of its component factors, and with a lower incidence of hypertension and diabetes. Our findings should be evaluated in large randomized trials of the effects of whole fat dairy on the risks of MetS, hypertension, and diabetes.
Isolation and next generation sequencing of archival formalin‐fixed DNA

DNA from archived organs is presumed unsuitable for genomic studies because of excessive formalin‐fixation. As next generation sequencing (NGS) requires short DNA fragments, and Uracil‐N‐glycosylase (UNG) can be used to overcome deamination, there has been renewed interest in the possibility of genomic studies using these collections. We describe a novel method of DNA extraction capable of providing PCR amplicons of at least 400 bp length from such excessively formalin‐fixed human tissues. When compared with a leading commercial formalin‐fixed DNA extraction kit, our method produced greater yields of DNA and reduced sequence variations. Analysis of PCR products using bacterial sub‐cloning and Sanger sequencing from UNG‐treated DNA unexpectedly revealed increased sequence variations, compared with untreated samples. Finally, whole exome NGS was performed on a myocardial sample fixed in formalin for 2 years and compared with lymphocyte‐derived DNA (as a gold standard) from the same patient. Despite the reduction in the number and quality of reads in the formalin‐fixed DNA, we were able to show that bioinformatic processing by joint calling and variant quality score recalibration (VQSR) increased the sensitivity four‐fold to 56% and doubled specificity to 68% when compared with a standard hard‐filtering approach. Thus, high‐quality DNA can be extracted from excessively formalin‐fixed tissues and bioinformatic processing can optimise sensitivity and specificity of results. Sequencing of several sub‐cloned amplicons is an important methodological step in assessing DNA quality.
Mammalian target of rapamycin inhibitors after post-transplant hepatocellular carcinoma recurrence: Is it too late?

BACKGROUND Mammalian target of rapamycin (mTOR) inhibitors have been shown to reduce the risk of tumour recurrence after liver transplantation for hepatocellular carcinoma (HCC). However, their role in established post-transplant HCC recurrence is uncertain. AIM To investigate whether mTOR inhibitor offers a survival benefit in post-transplant HCC recurrence. METHODS A retrospective study of 143 patients who developed HCC recurrence after liver transplantation was performed. They were divided into 2 groups based on whether they had received mTOR inhibitor-based immunosuppression. The primary endpoint was post-recurrence survival. RESULTS Seventy-nine (55%) patients received an mTOR inhibitor-based immunosuppressive regime, while 64 (45%) patients did not. The mTOR inhibitor group had a lower number of recurrent tumours (2 vs 5, P = 0.02) and received more active treatments including radiotherapy (39 vs 22%, P = 0.03) and targeted therapy (59 vs 23%, P < 0.001). The median post-recurrence survival was 21.0 ± 4.1 mo in the mTOR inhibitor group and 11.2 ± 2.5 mo in the control group. Multivariate Cox regression analysis confirmed that mTOR inhibitor therapy was independently associated with improved post-recurrence survival (P = 0.04, OR = 0.482, 95%CI: 0.241-0.966). The number of recurrent tumours and use of other treatment modalities did not affect survival. No survival difference was observed between mTOR inhibitor monotherapy and combination therapy with calcineurin inhibitor. CONCLUSION mTOR inhibitors prolonged survival after post-transplant HCC recurrence.
A method for using commercial ELISA tests to detect zoospores of Phytophthora and Pythium species in irrigation water

Commercially available ELISA tests for detecting Phytophthora and Pythium species were used to detect propagules of these genera in water samples. Samples were filtered through 0.45-μm filters to concentrate propagules before extraction. Heating filter residues to 100 C for 5 min yielded extracts that were equal or superior in reactivity to those obtained by liquid nitrogen disruption. As few as 30-40 zoospore cysts were detected in filter pad extracts. Detection sensitivity (propagules per liter) depends on the volume of water that can be passed through the filters (.)
Photosynthesis and inorganic carbon utilization in Pleurochrysis sp. (Haptophyta), a coccolithophorid alga

We studied and compared properties of inorganic carbon fixation for 2 coccolithophorid strains that differ in their capacity to calcify; namely high calcifying (HC) Pleurochrysis sp. CCMP 299 and low calcifying (LC) Pleurochrysis elongata CCAP 961/3. Pleurochrysis species are unicellular algae that, in nature and in culture, produce intracellular CaC03 encrusted structures (coccoliths). Pleurochrysis, and other calcifying algae, are potential players in atmospheric CO2 cycling and the maintenance of global carbon balances. In Pleurochrysis sp, and P. elongata (hereafter Pleurochrysis), photosynthesis was affected by increasing O2 (from 1 to 21 % in air), with 18% inhibition for LC cells and 9 % for HC cells. The inhibition could be reversed by (1) decreasing the ambient 02, (2) reducing the ambient pH (which rose in the medium, particularly for LC cells) and (3) by increasing the ambient inorganic carbon concentration. Carbonic anhydrase activity was detected in Pleurochrysis; HC cells having approximately 4 times more activity than LC cells. Inhibition of carbonic anhydrase by 0.25 mM acetazolamide (a non-membrane-permeating inhibitor of the enzyme) averaged 30% in HC cells and only 10% in LC cells. Calcium uptake measured for HC cells was 2.5 to 3.0 times higher in the light and 4 times higher in the dark than calcium uptake measured for LC cells. Rates of photosynthetic 0, evolution were significantly higher for both strains at acidic pH (e.g. 5.0, containing about 90% COz) than at seawater pH (e.g. 8.0, having about 1 % CO,), while at a basic pH (e.g. 9.0, virtually no CO2 and about 50% HC03-) rates were still substantial for HC cells but extremely low for LC cells. These data indicate that HC cells in their natural environment are primarily HC03users. By comparing seawater COz concentrations (i.e. 15 FM) with calculated KO,(CO2), the CO2 concentration required for a halfmaximal rate of photosynthetic O2 evolution, for Pleurochrysis (51 and 37 pM for HC and LC cells, respectively) it follows that CO2 must be concentrated intracellularly for effective photosynthesis in both strains. Thus, an adequate CO2 supply depends on HC03utilization and concomitant calcification, particularly in HC cells.