Miracle-dz/UniFAR-FTUs huggingface dataset:
PHYLOGENY OF THE GENUS EREMURUS (ASPHODELACEAE) BASED ON MORPHOLOGICAL CHARACTERS IN THE FLORA IRANICA AREA

,A phylogenetic analysis of Eremurus (Asphodelaceae) based on morphological data is presented. A total of twentyfive characters including 20 gross morphological, 4 palynological and 1 chromosomal characters were analyzed to reconstruct phylogenetic relationships for 24 taxa of Eremurus and Trachyandra malosana plus Asphodelus tenuifolius and two Asphodeline species as outgroups. Maximum parsimony approach as implemented in PAUP* using heuristic search and branch swapping option of tree bisection-reconnection were used for phylogenetic analyses. The analysis of characters with successive weighting using rescaled consistency index generated more resolved and supported trees than the analysis with equally weighting characters. The analyses showed that T. malosana is well allied with a clade of Eremurus species. Among Eremurus species analyzed, E. persicus and a subclade of E. kopetdaghensis and E. luteus comprise the basal most branches as sisters to the remainder. Eremurus subgenus Henningia with 15 taxa was paraphyletic; whereas, nine members of Eremurus subgenus Eremurus formed a well supported monophyletic group for which E. furseorum of the former subgenus was sister taxon. Sections Henningia (of subgenus Henningia) and Eremurus (of subgenus Eremurus) are also appeared to be nonmonophyletic while the section Ammolirion (of subgenus Eremurus) is monophyletic. Medium size pollen grain, (25-50 µm) and chromosome number of 2n=14 are shared by Eremurus and Trachyandra. Three characters including non-branched inflorescence, basifixed stamens and ellipsoidal pollen grains are synapomorphies for the genus Eremurus solely. Tubular/campanulate flowers, incurved tepals and tepals with 3-5 nerves are synapomorphies for the subgenus Eremurus. Similarly exerted stamen is a synapomorphy for the subgenus Eremurus and E. forseorum (from subgenus Henningia). The tubular flowers (rather than campanulate) and the thinnest pollen exine are putative synapomorphies for the section Ammolirion. The remaining characters were evolved homoplasiously or ambiguously among these taxa.
Mapping Benthic Habitats by Extending Non-Negative Matrix Factorization to Address the Water Column and Seabed Adjacency Effects

Monitoring of coastal areas by remote sensing is an important issue. The interest of using an unmixing method to determine the seabed composition from hyperspectral aerial images of coastal areas is investigated. Unmixing provides both seabed abundances and endmember reflectances. A sub-surface mixing model is presented, based on a recently proposed oceanic radiative transfer model that accounts for seabed adjacency effects in the water column. Two original non-negative matrix factorization ( N M F )-based unmixing algorithms, referred to as W A D J U M (Water ADJacency UnMixing) and W U M (Water UnMixing, no adjacency effects) are developed, assuming as known the water column bio-optical properties. Simulations show that W A D J U M algorithm achieves performance close to that of the N M F -based unmixing of the seabed without any water column, up to 10 m depth. W U M performance is lower and decreases with the depth. The robustness of the algorithms when using erroneous information about the water column bio-optical properties is evaluated. The results show that the abundance estimation is more reliable using W A D J U M approach. W A D J U M is applied to real data acquired along the French coast; the derived abundance maps of the benthic habitats are discussed and compared to the maps obtained using a fixed spectral library and a least-square ( L S ) estimation of the seabed mixing coefficients. The results show the relevance of the W A D J U M algorithm for the local analysis of the benthic habitats.
Physical Function Impairment and Frailty in Middle-Aged People Living With Human Immunodeficiency Virus in the REPRIEVE Trial Ancillary Study PREPARE.

BACKGROUND People with human immunodeficiency virus (PWH) are at risk for accelerated development of physical function impairment and frailty; both associated with increased risk of falls, hospitalizations, and death. Identifying factors associated with physical function impairment and frailty can help target interventions. METHODS The REPRIEVE trial enrolled participants 40-75 years of age, receiving stable antiretroviral therapy with CD4+ T-cell count >100 cells/mm3, and with low to moderate cardiovascular disease risk. We conducted a cross-sectional analysis of those concurrently enrolled in the ancillary study PREPARE at enrollment. RESULTS Among the 266 participants, the median age was 51 years; 81% were male, and 45% were black, and 28% had hypertension. Body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) was 25 to <30 in 38% and ≥30 in 30%, 33% had a high waist circumference, 89% were physically inactive, 37% (95% confidence interval, 31%, 43%) had physical function impairment (Short Physical Performance Battery score ≤10), and 6% (4%, 9%) were frail and 42% prefrail. In the adjusted analyses, older age, black race, greater BMI, and physical inactivity were associated with physical function impairment; depression and hypertension were associated with frailty or prefrailty. CONCLUSIONS Physical function impairment was common among middle-aged PWH; greater BMI and physical inactivity are important modifiable factors that may prevent further decline in physical function with aging. CLINICAL TRIALS REGISTRATION NCT02344290.
Effect of feed cycling on specific growth rate, condition factor and RNA/DNA ratio of Labeo rohita

A study was conducted to evaluate the effect of feed cycling on specific growth rate, condition factor and RNA/DNA ratio of Labeo rohita. Fingerling L. rohita were randomly collected from Qadria Fish Farm and Hatchery, Multan, Pakistan and divided into control, 5 days and 10 days feed cycling groups. Specific growth rate (% g day-1), body composition, condition factor, and RNA/DNA ratio of individual fish and of each group were calculated. There was a highly significant (P<0.001) effect of feed cycling on specific growth rate and RNA/DNA ratio of L. rohita. However, the effect on condition factor was non-significant. A gradual decline was observed in specific growth rate and RNA/DNA ratio with increasing length of starvation. L. rohita was able to maintain its main body constituents such as fat, protein, organic and inorganic contents indicating a compensatory growth, which was independent of duration of starvation
Efficacy of Erymicin 200 Injections for Reducing Renibacterium salmoninarum and Controlling Vertical Transmission in an Inland Rainbow Trout Brood Stock

Bacterial Kidney Disease, caused by Renibacterium salmoninarum (Rs), is widespread and can cause significant mortality at most life stages in infected salmonids. Rs is commonly found in inland trout, which can be carriers of the bacterium. Lethal spawns can be used to control vertical transmission to progeny through the culling of eggs from infected parents, but can be costly, time-consuming, and can negatively impact important and rare brood stocks. Erymicin 200 is an Investigational New Animal Drug (INAD) intended to reduce Rs levels in hatchery brood stocks and control vertical transmission to progeny. We tested the efficacy of Erymicin 200 injections in a positive, hatchery-resident rainbow trout (Oncorhynchus mykiss) brood stock in Colorado, USA. Brood fish age two and three were injected with 25 mg per kg of body weight Erymicin 200 three times prior to spawning. Erymicin 200 was effective in reducing Rs to below detectable levels in treated fish. However, both negative treated and control brood fish produced positive progeny, suggesting that Erymicin 200 did not prevent the vertical transmission of Rs.
Head and Neck Multi-Organ Auto-Segmentation on CT Images Aided by Synthetic MRI.

PURPOSE Segmentation of organs-at-risk (OARs) is a weak link in radiotherapy treatment planning process because the manual contouring process is labor-intensive and time-consuming. This work aimed to develop a synthetic MR (sMR)-aided dual pyramid network (DPN) for rapid and accurate head and neck multi-organ segmentation that can expedite the treatment planning process. METHODS Forty-five patients' CT, MR and manual contours pairs were included as training dataset. Nineteen OARs were target organs to be segmented. The proposed sMR-aided DPN method is featured with a deep attention strategy to effectively segment multiple organs. Performance of the proposed method was evaluated using five metrics, including Dice similarity coefficient (DSC), Hausdorff distance 95% (HD95), mean surface distance (MSD), residual mean square distance (RMSD) and volume difference. The method was further validated by using the 2015 head and neck challenge data. RESULTS The contours generated by the proposed method closely resemble the ground-truth manual contours, as evidenced by encouraging quantitative results in terms of DSC using the 2015 head and neck challenge data. Mean DSC values of 0.91 ± 0.02, 0.73 ± 0.11, 0.96 ± 0.01, 0.78 ± 0.09/0.78 ± 0.11, 0.88 ± 0.04/0.88 ± 0.06 and 0.86 ± 0.08/0.85 ± 0.1 were achieved for brain stem, chiasm, mandible, left/right optic nerve, left/right parotid, and left/right submandibular, respectively. CONCLUSIONS We demonstrated the feasibility of sMR-aided DPN for head and neck multi-organ delineation on CT images. Our method has shown superiority over the other methods on the 2015 head and neck challenge data results. The proposed method could significantly expedite the treatment planning process by rapidly segmenting multiple OARs.
Associations of perceived adverse lifetime experiences with brain structure in UK Biobank participants.

BACKGROUND Adversity experiences (AEs) are major risk factors for psychiatric illness, and ample evidence suggests that adversity-related changes in brain structure enhance this vulnerability. To achieve greater understanding of the underlying biological pathways, increased convergence among findings is needed. Suggested future directions may benefit from the use of large population samples which may contribute to achieving this goal. We addressed mechanistic pathways by investigating the associations between multiple brain phenotypes and retrospectively reported AEs in early life (child adversity) and adulthood (partner abuse) in a large population sample, using a cross-sectional approach. METHODS The UK Biobank resource was used to access imaging-derived phenotypes (IDPs) from 6,751 participants (aged: M = 62.1, SD = 7.2, range = 45-80), together with selected reports of childhood AEs and adult partner abuse. Principal component analysis was used to reduce the dimensionality of the data prior to multivariate tests. RESULTS The data showed that participants who reported experiences of childhood emotional abuse ('felt hated by family member as a child') had smaller cerebellar and ventral striatum volumes. This result was also depicted in a random subset of participants; however, we note small effect sizes ( η p 2 < .01), suggestive of modest biological changes. CONCLUSIONS Using a large population cohort, this study demonstrates the value of big datasets in the study of adversity and using automatically preprocessed neuroimaging phenotypes. While retrospective and cross-sectional characteristics limit interpretation, this study demonstrates that self-perceived adversity reports, however nonspecific, may still expose neural consequences, identifiable with increased statistical power.
Alcohol Misuse and Women’s Use of Aggression in Intimate Relationships: The Mediating Role of Motivations for Using Aggression

The relationship between alcohol misuse and women’s use of intimate partner violence (IPV) aggression has been well studied; however, there has been no research to date on women’s self-reported motivations for use of IPV aggression (e.g., self-defense, control) as an underlying mechanism explaining this link. Accordingly, this study aims to examine whether the effects of alcohol misuse on IPV aggression vary as a function of women’s motivations for using aggression. Participants were 412 ethnically diverse community women, between the ages of 18 and 65, in intimate relationships characterized by bidirectional IPV. The Motives and Reasons for IPV Scale was used to assess women’s reasons for using IPV aggression. Results revealed that the tough guise motive (i.e., wanting to appear tough, intimidating, and willing to harm one’s partner) explained the relationship between alcohol misuse and physical and sexual IPV aggression. Findings suggest the utility of incorporating the assessment of women’s motivations for IPV aggression in an effort to provide better informed intervention addressing the underlying reasons women use IPV aggression.
Phenolic contents, antioxidant activities and potential bioaccessibilities of industrial pomegranate nectar processing wastes

Summary Antioxidant potential and bioaccessibility of co-products from industrial pasteurised pomegranate nectar (PN) processing such as peel (PP), press cake (PC) and precipitate after clarification (PAC) in comparison with raw material (arils) and final products (CON and PN) were determined. Total phenolic (TPC), flavonoid (TFC), anthocyanin (TAC), tannin contents (TTC) and antioxidant activity (TAA) were determined besides identifying major phenolics and investigating in vitro bioaccessibility after gastrointestinal (GI) digestion. PP showed the highest values, except for TAC. Phenolics (12.7–43.0%) were found to be more stable than anthocyanins (0.6–2.1%) after in vitro GI digestion. PAC was found to be a better source for anthocyanins than CON and also showed higher phenolic bioaccessibility (28.8%) than PN (19.6%). PC and PAC possessed as much TPC, TFC, TTC and TAA levels as CON, with some exceptions. Therefore, these results indicated that not only PP but also PC and PAC should be valorised as a good source for phenolics and anthocyanins.
Enhanced Antiretroviral Therapy in Rhesus Macaques Improves RT-SHIV Viral Decay Kinetics

ABSTRACT Using an established nonhuman primate model, rhesus macaques were infected intravenously with a chimeric simian immunodeficiency virus (SIV) consisting of SIVmac239 with the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase from clone HXBc2 (RT-SHIV). The impacts of two enhanced (four- and five-drug) highly active antiretroviral therapies (HAART) on early viral decay and rebound were determined. The four-drug combination consisted of an integrase inhibitor, L-870-812 (L-812), together with a three-drug regimen comprising emtricitabine [(−)-FTC], tenofovir (TFV), and efavirenz (EFV). The five-drug combination consisted of one analog for each of the four DNA precursors {using TFV, (−)-FTC, (−)-β-d-(2R,4R)-1,3-dioxolane-2,6-diaminopurine (amdoxovir [DAPD]), and zidovudine (AZT)}, together with EFV. A cohort treated with a three-drug combination of (−)-FTC, TFV, and EFV served as treated controls. Daily administration of a three-, four-, or five-drug combination of antiretroviral agents was initiated at week 6 or 8 after inoculation and continued up to week 50, followed by a rebound period. Plasma samples were collected routinely, and drug levels were monitored using liquid chromatography-tandem mass spectrometry (LC–MS-MS). Viral loads were monitored with a standard TaqMan quantitative reverse transcriptase PCR (qRT-PCR) assay. Comprehensive analyses of replication dynamics were performed. RT-SHIV infection in rhesus macaques produced typical viral infection kinetics, with untreated controls establishing persistent viral loads of >104 copies of RNA/ml. RT-SHIV loads at the start of treatment (V0) were similar in all treated cohorts (P > 0.5). All antiretroviral drug levels were measureable in plasma. The four-drug and five-drug combination regimens (enhanced HAART) improved suppression of the viral load (within 1 week; P < 0.01) and had overall greater potency (P < 0.02) than the three-drug regimen (HAART). Moreover, rebound viremia occurred rapidly following cessation of any treatment. The enhanced HAART (four- or five-drug combination) showed significant improvement in viral suppression compared to the three-drug combination, but no combination was sufficient to eliminate viral reservoirs.
Environmentally friendly processes from coffee wastes to trimethylolpropane esters to be considered biolubricants

ABSTRACT In this study, an eco-friendly renewable biodegradable alternative to petroleum-based oil lubricants was produced using espresso coffee wastes. Waste coffee oil used as raw material was extracted from Espresso coffee wastes by Soxhlet and conventional solvent extraction. Free fatty acids (FFA) were obtained by hydrolysis of the obtained waste oil using Lipozyme TL IM (Thermomyces lanuginosus). The byproduct, glycerol, was also separated from the reaction medium using a separatory funnel. The obtained FFA was used as a raw material in the production of TMP esters. Polyol esters of fatty acids were synthesized as a result of the esterification reaction between FFA and polyol alcohol (trimethylolpropane (TMP)) using Novozyme 435 (Candida antarctica). The amount of FFA in the medium and the FFA conversion was determined by titration with NaOH solution according to ASTM D 5555–95 standard and the FFA composition of espresso coffee oil by GC. The oil content of espresso coffee extract was found to be rich by 16% and the FFA composition was rich in palmitic acid (C16:0 43% by weight) and linoleic acid (C18:2 31% by weight). 31% of FFA was obtained from the coffee oil. Experimental studies have shown that the highest FFA conversion of 88% with 93% TMP tri-ester content was obtained at a temperature of 55°C, 5% enzyme (w/w), non-aqueous media, 3/1 FFA/TMP mole ratio, 500 rpm mixing speed and 24 hours. Implications: Filter coffee wastes, which have become one of the most important biological wastes with an annual production capacity of 6 million tons worldwide; It is targeted to be transformed into environmentally friendly products, as it is important in terms of economy and policies of many developing countries, it is a renewable resource and there is a high amount of waste accumulation day by day. Evaluation of waste filter coffees and oils with this research article; It is envisaged that the bio-lubricating oil used in many sectors will be synthesized and commercialized with an environmentally friendly process.
Complete Genome Sequence of Clostridium innocuum Strain LC-LUMC-CI-001, Isolated from a Patient with Recurrent Antibiotic-Associated Diarrhea

Here, we report the complete genome sequence of Clostridium innocuum strain LC-LUMC-CI-001. As recently as 2018, C. innocuum was generally considered a benign gastrointestinal microorganism. This strain was isolated from the stool of a patient with recurrent Clostridioides difficile infection-like illnesses. ABSTRACT Here, we report the complete genome sequence of Clostridium innocuum strain LC-LUMC-CI-001. As recently as 2018, C. innocuum was generally considered a benign gastrointestinal microorganism. This strain was isolated from the stool of a patient with recurrent Clostridioides difficile infection-like illnesses.
Association between marijuana use and electrocardiographic abnormalities by middle age The Coronary Artery Risk Development in Young Adults (CARDIA) Study.

AIMS To evaluate the prevalence of electrocardiogram (ECG) abnormalities in marijuana users as an indirect measure of subclinical cardiovascular disease (CVD). DESIGN Longitudinal and cross-sectional secondary data analysis from the CARDIA (Coronary Artery Risk Development in Young Adults) study. SETTING 4 communities in the United States. PARTICIPANTS A total of 2,585 participants from the 5,115 black and white men and women recruited at age 18 to 30 years in 1985 to 1986 in CARDIA. MEASUREMENTS ECG abnormalities coded as minor and major abnormalities with the Minnesota code of electrocardiographic findings at Year 20. Self-reported current (past 30 days) and computed cumulative lifetime marijuana use (one "marijuana-year" corresponds to 365 days of use) through assessments every 2-5 years. We fitted logistic regression models adjusting for sex, race, center, education, age, tobacco smoking, physical activity, alcohol use, and body mass index. FINDINGS Among the 2,585 participants with an ECG at Year 20, mean age was 46, 57% were women, 45% were black. 83% had past exposure to marijuana and 11% were using marijuana currently. One hundred and seventy-three participants (7%) had major abnormalities and 944 (37%) had minor abnormalities. Comparing current with never use in multivariable-adjusted models, the OR for major ECG abnormalities was 0.60 (95% CI: 0.32 to 1.15) and for minor ECG abnormalities 1.21 (95% CI: 0.87 to 1.68). Results did not change after stratifying by sex and race. Cumulative marijuana use was not associated with ECG abnormalities. CONCLUSION In a middle-aged US population, lifetime cumulative and occasional current marijuana use were not associated with increases in electrocardiogram abnormalities. This adds to the growing body of evidence that occasional marijuana use and cardiovascular disease events and markers of subclinical atherosclerosis are not associated.
High genetic diversity in a world-wide collection of Lathyrus sativus L. revealed by isozymatic analysis

Abstract Grasspea (Lathyrus sativus L.) is an annual, herbaceous, drought-resistant legume and staple crop in Asian and African countries. Little is known about the nature and the amount of genetic diversity present in existing grasspea seed collections, yet this information is pivotal for future breeding programmes, such as those striving to reduce high neurotoxin levels present in seeds. Here we report on the level of genetic diversity within a world-wide collection of L. sativus, determined by isozymatic analysis. Although grasspea is generally considered a predominantly self-pollinating species, we found that the population genetic structure of these accessions showed a considerable outcrossing rate of 36%. The identification of a mixed mating system in L. sativus has significant implications for collecting and multiplying genetic resources for conservation and for future breeding purposes. In addition, we determined the genetic closeness of grasspea accessions from different geographical regions around the world. While we noticed an allelic richness in this species that was conserved across the regions, we did not find any evidence of high genetic identity between accessions, even when originating from the same geographical location. Instead, we found that greater genetic variability existed at the intra-regional level than at the inter-regional level.