Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematics and biogeography of palearctic avifauna : evolution, hybridisation and secondary contact zones

A database was created of digitized equal area distribution maps of 3,036 phylogenetic species of Palearctic songbirds. Biogeographic patterns are reported for two data sets: (1) including all passeriform bird species reported as breeding within the boundaries of our study map, (2) passeriform species restricted in their distribution to our study region, thus excluding the partly extra-limital taxa. With respect to the data set excluding partly extralimital taxa, the average range size is 238 grid cells (grid cell area: 4,062 km). Analysis of the geographic distribution of species richness for the full data set showed several hotspot regions, mostly located in mountainous areas. The index of range-size rarity identified similar hotspot regions as that for species richness, albeit that the range-size rarity deemphasized the central Siberian hotspot. Range-size rarity hotspots that are not evident on the measure of species richness concern a great number of islands. Much more prominent on the index of range-size rarity are the Atlas Mountains of northern Africa, the Jabal al Akhdar region in NE Libya, and the eastern border of the Mediterranean. Restricting the analysis of geographic variation to the 25% of the species with smallest ranges resulted in a greatly simplified pattern of hotspots.
Effects of composite casein and P-lactoglobulin genotypes on renneting properties and composition of bovine milk by assuming an animal model

The effects of K-p-casein genotypes and P-lactoglobulin genotypes on the renneting properties and composition of milk were estimated for 174 and 155 milk samples of 59 Finnish Ayrshire and 55 Finnish Friesian cows, respectively. As well as the random additive genetic and permanent environmental effects of a cow, the model included the fixed effects for parity, lactation stage, season, K-p--casein genotypes and P-lactoglobulin genotypes. Favourable renneting properties were associated with K-P-casein genotypes ABA,A, and AAA,A 2 in the Finnish Ayrshire, and with ABA 2 8, AAA, A,, AAA 2 A 3 , ABA,A, and ABA 2 A 2 in theFinnish Friesian. The favourable effect of these gen- otypes on curd firming time and on firmness of the curd was partly due to their association with a high K-casein concentration in the milk. The effect of the K-casein E allele on renneting properties was unfavourable compared with that of the K-casein B allele, and possibly with that of the A allele. The P-lactoglobulin genotypes had no effect on renneting properties but they had a clear effect on the protein composition of milk. The P-lactoglobulin AA genotype was associated with a high whey protein % and P-lactoglobulin concentration and the BB genotype with a high casein % and casein number.
Invertebrate hydraulic preferences and predicted impacts of changes in discharge in a large river.

SUMMARY 1. Instream habitat models are attractive tools for assessing the impacts of flow restoration on aquatic organisms, but have been rarely used for invertebrates due to the lack of knowledge of their hydraulic preferences. 2. In this study, we provide quantitative models of the hydraulic preferences for 66 invertebrate taxa found in the Upper Rhone River (France), and combine these preferences with a statistical habitat model (FSTress) to predict the effects of minimum flow restoration on invertebrate abundances in two bypassed sections of the river. 3. Many taxa show marked preferences for particular hydraulic conditions. Average preferred hydraulic conditions were significantly related to those observed in smaller streams (R 2 = 0.37). 4. Our model predicted that habitat values of 27 taxa should be enhanced by restoration operations, but also predicted a decrease of habitat values in the main channel for 12 limnophilic taxa. However, these taxa are expected to maintain populations by finding refuges in restored cut-off channels and overall invertebrate diversity is predicted to increase in the two bypassed sections studied here.
Mechanistic characterization of UDP‐glucuronic acid 4‐epimerase

UDP‐glucuronic acid (UDP‐GlcA) is a central precursor in sugar nucleotide biosynthesis and common substrate for C4‐epimerases and decarboxylases releasing UDP‐galacturonic acid (UDP‐GalA) and UDP‐pentose products, respectively. Despite the different reactions catalyzed, the enzymes are believed to share mechanistic analogy rooted in their joint membership to the short‐chain dehydrogenase/reductase (SDR) protein superfamily: Oxidation at the substrate C4 by enzyme‐bound NAD+ initiates the catalytic pathway. Here, we present mechanistic characterization of the C4‐epimerization of UDP‐GlcA, which in comparison with the corresponding decarboxylation has been largely unexplored. The UDP‐GlcA 4‐epimerase from Bacillus cereus functions as a homodimer and contains one NAD+/subunit (kcat = 0.25 ± 0.01 s−1). The epimerization of UDP‐GlcA proceeds via hydride transfer from and to the substrate’s C4 while retaining the enzyme‐bound cofactor in its oxidized form (≥ 97%) at steady state and without trace of decarboxylation. The kcat for UDP‐GlcA conversion shows a kinetic isotope effect of 2.0 (±0.1) derived from substrate deuteration at C4. The proposed enzymatic mechanism involves a transient UDP‐4‐keto‐hexose‐uronic acid intermediate whose formation is rate‐limiting overall, and is governed by a conformational step before hydride abstraction from UDP‐GlcA. Precise positioning of the substrate in a kinetically slow binding step may be important for the epimerase to establish stereo‐electronic constraints in which decarboxylation of the labile β‐keto acid species is prevented effectively. Mutagenesis and pH studies implicate the conserved Tyr149 as the catalytic base for substrate oxidation and show its involvement in the substrate positioning step. Collectively, this study suggests that based on overall mechanistic analogy, stereo‐electronic control may be a distinguishing feature of catalysis by SDR‐type epimerases and decarboxylases active on UDP‐GlcA.
Women’s knowledge and its associated factors regarding optimum utilisation of antenatal care in rural Ghana: A cross-sectional study

Introduction Improving maternal health is a global public health challenge especially in sub-Saharan Africa. The optimum utilisation of antenatal care (ANC) by pregnant women is known to improve maternal health outcomes. Maternal morbidity and mortality rates in Ghana remain unacceptably high, particularly in rural settings where skilled delivery care often times is disproportionally low. This study assessed factors associated with optimum utilisation of antenatal care in rural Ghana. Methods A cross-sectional design was applied to collect data among eligible participants between October 2018 and January 2019. A total of 322 women who gave birth and attended the postnatal clinic were recruited for the study. Consecutive sampling was employed in recruiting participants. The associations between the dependent variables (ANC service utilisation and knowledge of ANC) and independent variables (socio-demographic characteristics) were examined using ordinary least squares logistic regression at 95% confidence interval in STATA version 14.0. Results Of the 322 participants, 69.0% reported utilising at least four or more times ANC services. Determinants of women attending ANC for four or more times was significantly associated with age [OR = 4.36 (95%CI: 2.16–8.80), p<0.001], educational level [OR = 10.18 (95%CI: 3.86–26.87), p<0.001], and insured with National Health Insurance Scheme [OR = 3.42 (95%CI: 1.72–6.82), p<0.001]. Not married [OR = 0.65 (0.39–1.09), p = 0.011] or divorced [OR = 0.33 (95%CI: 0.13–0.83), p = 0.019] was negatively associated with utilisation of four or more ANC services. The majority (79.0%) of the participants had a good level of knowledge regarding antenatal care. Conclusion Although the majority of women in this study had good knowledge of ANC services, a significant number of them did not complete the recommended number of ANC visits for at least four times during a normal pregnancy. Awareness and further education to reproductive-age women on the significant role adequate ANC attendance plays in advancing health and well-being require further investments, particularly among rural women in Ghana.
Eating disorders during the COVID-19 pandemic and quarantine: an overview of risks and recommendations for treatment and early intervention

ABSTRACT Individuals with eating disorders (EDs) are at significant risk for increases in symptomatology and diminished treatment access during the COVID-19 pandemic. Environmental precautions to limit coronavirus spread have affected food availability and access to healthy coping mechanisms, and have contributed to weight-stigmatizing social media messages that may be uniquely harmful to those experiencing EDs. Additionally, changes in socialization and routine, stress, and experiences of trauma that are being experienced globally may be particularly deleterious to ED risk and recovery. This paper presents a brief review of the pertinent literature related to the risk of EDs in the context of COVID-19 and offers suggestions for modifying intervention efforts to accommodate the unique challenges individuals with EDs and providers may be experiencing in light of the ongoing public health crisis.
Predicting Odontogenic Sinusitis in Unilateral Sinus Disease: A Prospective, Multivariate Analysis

Background Odontogenic sinusitis (ODS) is a common cause of unilateral sinus disease (USD), but can be challenging to diagnose due to nonspecific clinical presentations, potentially subtle to absent dental pathology on sinus computed tomography (CT), and underrepresentation in the sinusitis literature. Objective Identify sinonasal clinical variables predictive of ODS in patients presenting with unilateral maxillary sinus opacification on sinus CT. Methods A prospective cohort study was conducted on 131 consecutive patients with USD and at least partial or complete maxillary sinus opacification on sinus CT. Patients’ demographics, sinonasal symptoms (anterior and posterior drainage, nasal obstruction, facial pressure, smell loss, and foul smell), 22-item sinonasal outcome test, nasal endoscopy findings, CT findings, and histopathology were collected. Patients’ diagnoses included ODS, chronic rhinosinusitis with or without nasal polyps, and inverted papilloma. Demographic and clinical data were compared between patients with unilateral ODS and non-odontogenic disease using univariate and multivariate analyses. Results Of the 131 USD patients, 65 had ODS and 66 had non-odontogenic disease. The following variables were significantly associated with unilateral ODS on multivariate analysis: middle meatal pus on endoscopy (OR= 17.67, 95% CI-5.69, 54.87; p = 0.001), foul smell (OR= 6.11, 95% CI-1.64, 22.82; p=.007), facial pressure (OR= 3.55, 95% CI-1.25, 10.12; p = 0.018), and any frontal opacification on CT (OR= 5.19, 95% CI-1.68, 16.06; p = 0.004). Any sphenoid opacification on CT was inversely related to ODS (OR = 0.14, 95% CI-0.03, 0.69; p = 0.016). The study was adequately powered. Conclusion With unilateral maxillary sinus disease, the following features were significantly associated with ODS: foul smell, ipsilateral facial pressure, middle meatal pus on endoscopy, and any frontal sinus opacification on sinus CT. Additionally, any sphenoid sinus opacification on CT was inversely related to ODS. Presence or absence of these clinical variables can be used to increase or decrease one’s suspicion of an odontogenic source of sinusitis.
Restriction fragment analysis of mitochondrial DNA in common murres, Uria aalge, from four Norwegian seabird colonies

Alcid species (auks) breed in a restricted number of large seabird colonies and are considered highly philopatric. Mitochondrial DNA (mtDNA) of Common Murres, Uria aalge, from four Norwegian colonies was investigated by restriction analysis to assess the amount of geographic population structure and genetic variability in a colonial breeder. Eleven restriction endonucleases revealed 13 mtDNA genotypes among 51 individuals. Genetic diversity was low, with an average of 0.11% (range 0.0–0.55%) sequence divergence between all individuals. Population divergence within the surveyed region seems to be minimal, demonstrated by the low levels of sequence divergence between colonies and lack of spatial structuring of genotypes. Such results can be expected if birds originated from a smaller ancestral population during glaciation, and may have been reinforced by repeated population bottlenecks and considerable gene flow between colonies.
In Vitro. Antimicrobial Activity of Some Libyan Medicinal Plant Extracts

Abstract In vitro. antimicrobial activity of 32 extracts (ethanol, hexane, chloroform, and methanol) from eight different Libyan medicinal plants, namely Artemisia herba-alba. Asso (Compositae), Globularia alypum. L. (Globulariaceae), Helichrysum stoechas. , DC. (Compositae), Peganum harmala. L. (Zygophyllaceae), Polygonum equisetiforme. Sibth. & Sm. (Polygonaceae), Pulicaria crispa. (Forssk.) Oliv. (Compositae), Rosmarinus officinalis. L. (Labiatae), and Thymus capitatus. Hoffmanns & Link. (Labiatae), was determined against seven bacteria and one yeast strain using the broth microdilution method. The results show that all plants tested possessed antimicrobial activity against at least one of the examined strains at a concentration ≤8 mg/ml. The extracts from H. stoechas. , P. equisetiforme. , P. crispa. , R. officinalis. , and T. capitatus. exhibited strongest activity against Gram-positive bacteria with minimum inhibitory concentrations (MICs) ranging from 0.5 to 8 mg/ml. Only a few extracts showed inhibitory activity against Gram-negative strains in this test, whereas those of the H. stoechas. and P. harmala. were among the strongest ones (MICs range 4–8 mg/ml). High anticandidal activity was observed for P. harmala. , P. crispa. , and T. capitatus. , with MICs ranging from 0.25 to 1 mg/ml.
Modification methods toward the production of porous starch: a review

Abstract Starch is a complex carbohydrate formed by the repeating units of glucose structure connected by the alpha-glycosidic linkages. Starch is classified according to their derivatives such as cereals, legumes, tubers, palms, fruits, and stems. For decades, native starch has been widely utilized in various applications such as a thickener, stabilizer, binder, and coating agent. However, starches need to be modified to enhance their properties and to make them more functional in a wide range of applications. Porous starch is a modified starch product which has attracted interest of late. It consists of abundant pores that are distributed on the granule surface without compromising the integrity of its granular structure. Porous starch can be produced either by enzymatic, chemical, and physical methods or a combination thereof. The type of starch and selection of the modification method highly influence the formation of pore structure. By carefully choosing a suitable starch and modification method, the desired morphology of porous starch can be produced and applied accordingly for its intended application. Innovations and technologies related to starch modification methods have evolved over the years in terms of the structure, properties and modification effects of different starch varieties. Therefore, this article reviews recent modification methods in developing porous starch from various origins.
Electrophysiological Responses from the Human Tongue to the Six Taste Qualities and Their Relationships with PROP Taster Status

Taste buds containing receptor cells that primarily detect one taste quality provide the basis for discrimination across taste qualities. The molecular receptor multiplicity and the interactions occurring between bud cells encode information about the chemical identity, nutritional value, and potential toxicity of stimuli before transmitting signals to the hindbrain. PROP (6-n-propylthiouracil) tasting is widely considered a marker for individual variations of taste perception, dietary preferences, and health. However, controversial data have been reported. We present measures of the peripheral gustatory system activation in response to taste qualities by electrophysiological recordings from the tongue of 39 subjects classified for PROP taster status. The waveform of the potential variation evoked depended on the taste quality of the stimulus. Direct relationships between PROP sensitivity and electrophysiological responses to taste qualities were found. The largest and fastest responses were recorded in PROP super-tasters, who had the highest papilla density, whilst smaller and slower responses were found in medium tasters and non-tasters with lower papilla densities. The intensities perceived by subjects of the three taster groups correspond to their electrophysiological responses for all stimuli except NaCl. Our results show that each taste quality can generate its own electrophysiological fingerprint on the tongue and provide direct evidence of the relationship between general taste perception and PROP phenotype.
An Analysis of Variability in “CatWalk” Locomotor Measurements to Aid Experimental Design and Interpretation

Abstract Preclinical studies in models of neurologic injury and disease rely on behavioral outcomes to measure intervention efficacy. For spinal cord injury, the CatWalk system provides unbiased quantitative assessment of subtle aspects of locomotor function in rodents and so can powerfully detect significant differences between experimental and control groups. Although clearly of key importance, summary group-level data can obscure the variability within and between individual subjects and therefore make it difficult to understand the magnitude of effect in individual animals and the proportion of a group that may show benefit. Here, we calculate reference change intervals (RCIs) that define boundaries of normal variability for measures of rat locomotion on the CatWalk. Our results indicate that many commonly-used outcome measures are highly variable, such that differences of up to 70% from baseline value must be considered normal variation. Many CatWalk outcome variables are also highly correlated and dependent on run speed. Application of calculated RCIs to open access data (https://scicrunch.org/odc-sci) on hindlimb stride length in spinal cord-injured rats illustrates the complementarity between group-level (16 mm change; p = 0.0009) and individual-level (5/32 animals show change outside RCI boundaries) analysis between week 3 and week 6 after injury. We also conclude that interdependence among CatWalk variables implies that test “batteries” require careful composition to ensure that different aspects of defective gait are analyzed. Calculation of RCIs aids in experimental design by quantifying variability and enriches overall data analysis by providing details of change at an individual level that complement group-level analysis.
Salt marshes and eutrophication: An unsustainable outcome

Most plant production by emergent coastal marshes occurs belowground. This belowground production adds to the accumulation of organic matter sustaining salt marshes as sea level rises, thus preventing excessive flooding, eventual plant death, and habitat loss. The ubiquitous nutrient enrichment of coastal salt marshes stimulating aboveground plant growth may result in higher rates of inorganic matter accumulation that compensates for marsh flooding caused by sea level rise. Results from several short‐term experiments, however, demonstrate that root and rhizome biomass and carbon accumulation is reduced with nutrient enrichment, suggesting that eutrophication of coastal waters may not be a compensatory counterbalance to the effects of global sea level rise on salt marshes. We show that the net effects of 36 yr of nutrient enrichment in replicated field experiments do not lead to higher organic or inorganic accumulation. Enrichment reduces organic matter belowground and may result in a significant loss in marsh elevation equivalent to about half the average global sea level rise rates. Sustaining and restoring coastal emergent marshes is more likely if they receive less, not more, nutrient loading.
Intraspecific Variation in Herbivory on Two Tropical Tree Species

Levels of herbivory on young and mature leaves were determined for two tree species, Trichilia cipo (Meliaceae) and Cecropia insignis (Moraceae), in a lowland rain forest of Panama. Saplings of both species were studied in light gaps, and in addition, Trichilia was studied in the understory. Rates of leaf damage by insects were measured on marked plants during four 3-wk sample periods conducted at 5-mo intervals. Mature leaves of Cecropia suffered average damage rates that were five times greater than those suffered by Trichilia; the reverse was true for young leaves. Patterns of intraspecific variation in herbivory on mature leaves were similar for the two species, despite differences in life history, habitat, defensive characteristics, and levels of damage. Variation among individuals at any one sample period was high. Damage levels during sequential samples were not significantly correlated within an individual but were highly variable. For each sample period, a dif- ferent group of individuals (with one exception) comprised the 20% most heavily grazed. These pat- terns of herbivory are discussed with respect to seasonal effects, possible causal mechanisms, and implications for escape from herbivores and selection of defenses.
Detection of fungal infection in Lolium perenne by Fourier transform infrared spectroscopy

Aims The goal of the study was to apply Fourier transform infrared (FTIR) spectroscopy followed be chemometrical data treatment for the differentiation of fungi-infected perennial ryegrass (Lolium perenne) from non-infected grass. Methods FTIR was used to rapidly discriminate between leaves of perennial ryegrass (Lolium perenne) infected by a fungal endophyte (Epichloe; asexual forms: Neotyphodium) and uninfected leaves. Besides drying and grinding of the sampled leaves, no other preparation steps were needed. FTIR measurements were performed in the attenuated total reflection (ATR) mode. Aliquots of powdered leaf samples were placed on a ZnSe crystal and the spectra collected followed by chemometrical analysis (multidimensional factor analysis, hierarchical cluster analysis). Important Findings ATR-FTIR allowed a rapid detection of fungal infections in the plant material and proved to be a fast and reliable tool for the differentiation of the plant biomass without the need of time-consuming sample preparation.