Miracle-dz/UniFAR-FTUs huggingface dataset:
A new species of the genus Oligodon Fitzinger, 1826 (Squamata: Colubridae) from Cu Lao Cham Islands, central Vietnam

A new kukri snake, Oligodon culaochamensis sp. nov., is described from Cu Lao Cham Islands, central Vietnam, based on the morphology of six specimens, including two males, three females and one juvenile. The new species belongs to the O. cyclurus group and differs from other congeners in this group by a combination of the following characters: medium size in adults (total length up to 582 mm); 17–19 dorsal scale rows at neck and midbody and 15 or 17 rows before vent; tail length/total length ratio 0.218–0.219 in males and 0.166–0.169 in females; ventrals 167–169 in males and 179–182 in females; subcaudals 63–66 in males and 51–52 in females; head scalation complete with a presubocular; 9–10 maxillary teeth, the posterior three being enlarged; nasal divided; temporal streak absent; long and deeply forked hemipenes extending to 20 th subcaudal and without spines and papillae but with prominent diagonal ridge, oblique flounces and distal calyces; cloacal plate undivided; 10–11+3–4 dorsal blotches; and a vertebral stripe on tail and anterior part of body. This is the second species of Oligodon described on islands of Vietnam.
The molecular landscape of HPV-driven tumourigenesis

Human Papillomaviruses (HPV) contribute significantly to the global cancer burden, causing nearly all cervical cancers and varying proportions of head and neck, and other anogenital cancers. Previous studies, limited to small sample sizes or single tissue sites in studies, have suggested that HPV+ tumours can exhibit distinct molecular profiles. Initially, a comprehensive transcriptional signature was established for HPV-driven tumourigenesis and culminated in the confirmation of a driver role for HPV outside the Oropharynx in Head and Neck cancer and the discovery of prognostically relevant differences in the immune microenvironment with implications for patient management. Analysis of exomes for mutagenesis by APOBEC3B, found upregulated in HPV+ tumours, identified it as a key driver of genomic evolution in these tumours, and broadly as a determinant of hotspot specificity in PIK3CA mutations across cancers. Establishment of HPV-associated DNA methylation signatures, useful for classification, also highlighted novel HPV-related transcriptional changes and putative heterogeneity in cell-of-origin associated with HPV types and tissue sites. Analyses of transcriptional and epigenetic heterogeneity in Cervical Cancer, where multiple HPV types are causal, identified HPV45-associated molecular signatures indicative of increased invasiveness and inflammation with putative applications in patient stratification. Finally, Support Vector Regression approaches developed to perform deep deconvolution of the cellular composition of tumours facilitated integrative analysis of immune cell infiltration patterns, the prognostic patterns discovered in the thesis and molecular variation, offering insights into the role of the immune microenvironment in shaping the evolution of these tumours.
In Vivo Measurements of the Frequency-Dependent Impedance of the Spinal Cord

Improved knowledge of the electrode-tissue impedance will be useful in optimizing the clinical protocols and resulting efficacy of the existing and emerging approaches to spinal cord stimulation. Toward that end, the complex impedance (amplitude and phase) of in vivo ovine spinal cord tissue was measured at the electrode-pial subdural surface interface from 5 Hz to 1 MHz, and with the bi-polar electrodes oriented both parallel and perpendicular to the rostral-caudal axis of the spinal cord. At stimulation frequencies above 10 kHz, most of the impedance then becomes resistive in nature and the phase diference between the stimulation signal and the resulting current drops to ≈ 10˚, thus maximizing power transfer to the tissues. Also, at these higher frequencies, the current pulse maintains significantly greater fidelity to the shape of the stimulation signal applied across the electrodes. Lastly, there were lower impedances associated with parallel as opposed to perpendicular orientation of the electrodes, thus reflecting the effects of fiber orientation within the spinal cord. Impedance differences of this kind have not been reported with epidural stimulation because of the electrical shunting effects of the intervening layer of relatively high conductivity cerebrospinal fluid. These observations provide a quantitative basis for improved models of spinal cord stimulation and suggest certain advantages for direct intradural stimulation relative to the standard epidural approaches. (Some figures in this article are in colour only in the electronic version)
Growth Performance, Fecal Noxious Gas Emission and Economic Efficacy in Broilers Fed Fermented Pomegranate Byproducts as Residue of Fruit Industry

Manuscript History: Byproducts of fruit industry are promising source of nutrients and bioactive compounds. The objective of the present experiment was to evaluate the effect of fermented pomegranate byproducts (FPB) on growth performance, fecal pH and noxious gas emissions; and economic efficacy in broilers. A feeding trial was carried out with 160 day old Ross broilers assigned to four dietary treatments having five replications (8 birds per replicate). The dietary treatments were control (T0), corn-soybean meal based basal diet; and test diets (T1 to T3), T1 = Basal diet + 0.5% FPB; T2 = Basal diet + 1.0% FPB; T3 = Basal diet + 2.0% FPB. The result revealed that, supplementation of FPB (T2 and T3) increased average daily weight gain of broilers during finisher and overall experimental period compared to control (T0) (P 0.05) among the dietary treatments. Fecal pH tended to reduce (P <0.05) in response to FPB supplemented group T1 and T3 compared to T0. In addition, fecal ammonia emission was lower (P <0.05) in all FPB supplemented groups (T1, T2 and T3), where hydrogen sulfide emission was reduced in T1 and T2 during incubation (P <0.05). Overall economic analysis indicated that, feed cost per unit of weight gain was lower (P <0.05) in the FPB supplemented T2 and T3 groups. Therefore, it could be concluded that FPB supplementation can significantly improve growth performance, reduce fecal pH and gas emission from excreta; and economical to utilize in broiler diet.
A new marine alga, Pterocladiella andresii sp. nov. (Gelidiales, Rhodophyta) and its relationship to P. caloglossoides from Pacific South America

The taxonomy of Pterocladiella from Pacific South America remains less studied. On the basis of morphological observations and mitochondrial cox 1 and plastid rbc L sequences, we describe a new species, P. andresii , from Chile and characterize recently collected specimens of P . caloglossoides from Peru, the first verified since Howe’s original collections of the type. Pterocladiella andresii is distinguished by small turfs of simple, narrow, compressed thalli that are rarely irregularly branched, and possess rhizines in the medulla, tetrasporangial sori with sterile a margin, and v-shaped to irregularly arranged tetrasporangia. New collections of Pterocladiella caloglossoides from northern Peru accord well with its original description. Both cox 1 and rbc L phylogenies revealed that P. andresii was sister to P. caloglossoides from Peru, and this group formed a clade with P. luxurians from California, USA. Morphological differences among P. andresii and its putative relatives are presented.
Patterns of species richness hotspots and estimates of their protection are sensitive to spatial resolution

Species richness is a measure of biodiversity often used in spatial conservation assessments and mapped by summing species distribution maps. Commission errors inherent those maps influence richness patterns and conservation assessments. We sought to further the understanding of the sensitivity of hotspot delineation methods and conservation assessments to commission errors, and choice of threshold for hotspot delineation.
Antimicrobial and Antioxidant Properties of Fruits of Capsicum annuum var. cerasiforme (Mill.) Irish and Heracleum nepalense D.Don

The fruit of Capsicum annuum var. cerasiforme belonging to the Family Solanaceae is a widely used spice in Sikkim, a North Eastern state of India. The fruit of Capsicum annuum var. cerasiforme locally called ‘Dalle Khorsani’ is a valuable cash crop of Sikkim and also possess medicinal properties. Heracleum nepalense D. Don locally called ‘Chimphing’ belongsto the Family Umbillifereae and is extensively used in folk medicine. The present study evaluated the antimicrobial property of fruits of Capsicum annuum var. cerasiforme (Mill.) Irish and Heracleum nepalense D. Don using agar well diffusion method against Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus vulgaris, Staphylococcus aureus, Bacillus cereus and Bacillus subtilis. The antioxidant property of methanol extracts of fruits of these test plants was also investigated. The antioxidant property was evaluated by 2, 2-diphenyl-1-picryl hydrazyl (DPPH) free radical scavenging activity assay and Ferric reducing power assay. The total phenolic content was determined by using Gallic acid as a standard. The methanol extract of both the plants inhibited the growth of mostly Gram positive bacteria and Escherichia coli among Gram negative bacteria. However the acetone extract of the selected plants did not exhibit antimicrobial activity. The methanol extracts of these plants exhibited significant (p>0.05) concentration dependent increase in DPPH free radical scavenging activity. The extract of Capsicum annuum var. cerasiforme (Mill.) Irish also exhibited significantly higher (p>0.05) ferric reducing ability thereby showing higher antioxidant activity. The phytochemical analyses of the plant extracts revealed the presence of phenol, tannin, flavonoid, alkaloid, steroid and saponin. The results of the present study indicate that Capsicum annuum var. cerasiforme (Mill.) Irish and Heracleum nepalense D. Don can be a potential source of antimicrobial and antioxidant agents and can be explored further for its therapeutic use.
Studying α-Synuclein pathology using iPSC-derived dopaminergic neurons

Parkinson's disease (PD) is characterised by the loss of dopaminergic neurons in the Substantia Nigra pars compacta in the midbrain and the presence of intracellular aggregates, known as Lewy bodies (LBs), in the surviving neurons. The aetiology of PD is unknown but a causative role for α-Synuclein (SNCA) has been proposed. Although the function of αSyn is not well understood, a number of pathological mechanisms associated with αSyn toxicity have been proposed. In this study, nine induced pluripotent stem cells (iPSCs) lines from healthy individuals and PD patients carrying the A53T SNCA mutation or a triplication of SNCA were differentiated to dopaminergic neurons (iDAn). All iPSC lines differentiated with similar efficiency to iDAn, indicating that they could be used for phenotypic analysis. Quantification of αSyn expression showed increased αSyn intracellular staining and the novel detection of increased αSyn oligomerization in PD iDAn. Analysis of mitochondrial respiration found a decrease in basal respiration, maximal respiration, ATP production and spare capacity in PD iDAn, but not in undifferentiated iPSCs, indicating the cell-type specificity of these defects. Decreased phosphorylation of dynamin-1-like protein at Ser616 (DRP1Ser616) and increased levels of Peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α) in A53T SNCA iDAn suggest a new pathological mechanism linking αSyn to the imbalance in mitochondria homeostasis. Markers of endoplasmic reticulum (ER) stress were found to be up-regulated, along with increased β- Glucocerebrosidase (GBA) activity, perturbation of autophagy and decreased expression of fatty acids binding protein 7 (FAPB7) in PD iDAn. Lastly, lentiviral vectors for RNAi-mediated knockdown of αSyn were developed and these reduced αSyn protein levels in iDAn, resulting in increased expression of FABP7. These results describe a novel functional link between αSyn and FABP7. This work demonstrates that iDAn are a promising and relevant in vitro cell model for studying cellular dysfunctions in PD pathology, and the phenotypic analysis of A53T SNCA and SNCA triplication iDAn enabled the detection of novel pathological mechanisms associated with PD.
Acrotomopus atropunctellus (Coleoptera: Curculionidae) Preference for Large Sugarcane Shoots Mitigates Damage to Sugarcane Crop

Summary The sugarcane weevil, Acrotomopus atropunctellus (Boheman) (Coleoptera: Curculionidae) is an increasingly important sugarcane pest in Argentina. Its emergence period overlaps with early stages of sugarcane phenology. This research assessed the preference of A. atropunctellus for shoot size and the effect of damage on shoot survival. Acrotomopus atropunctellus preferred to feed on large- and mediumsized shoots, regardless of sex. However, older plants were resistant to injury. Also, the number of punctures produced by females was 1.6 times greater than that produced by males. Avoiding late planting or harvest dates could be a useful tactic for mitigating A. atropunctellus incidence in sugarcane crops.
The complete mitochondrial genome of Cynoglossus joyneri and its novel rearrangement

Abstract The complete mitochondrial genome of Cynoglossus joyneri was determined. The length of the C. joyneri complete mitochondrial DNA sequence is 16,428 bp. The tRNA Gln gene is translocated from the light to the heavy strand (Q inversion), which is accompanied by shuffling of the tRNA Ile gene and long-range translocation of the putative control region downstream to a site between ND1 and the tRNA Gln gene, which is also seen in the closely related Cynoglossus semilaevis. C. joyneri has a closer relationship to Cynoglossus lineolatus and C. semilaevis, but had a distant relationship to Phoxinus percnurus and Sternula albifrons.
In Silico Binding Interactions Of Dehalogenase (Dehe) With Various Haloalkanoic Acids

Synthetic haloalkanoic acid (HA) is one of the synthetics compounds that can be found as active ingredients in herbicides. These compounds are known to pollute our agriculture land due to their toxicity, thus may cause serious environmental and health problems. Biological process such as microbial dehalogenation degrades the harmful compounds and prevents their migration into groundwater source. For instance, Rhizobial Dehalogenase E (DehE) could catalyze these HA compounds and convert them into hydroxylated compounds which are less harmful to the environment. In previous study, DehE was considered to degrade many HA compounds with different Km values. However, the binding interaction of this enzyme towards many HA substrates is still unclear. In this study, docking simulation has been performed to determine the affinity of active site residues of DehE towards 15 HA compounds. Tribromoacetic acid (TBA) was identified to be the most favourable substrate for DehE which has the lowest binding energy (-6.48 Kcal/mol) compared to other haloalkanoic acids. Size of halogen and hydrogen bond numbers are the contributing factor for dehalogenase affinity towards its substrates. Besides, it was found that Trp34, Phe37 and Ser188 served as binding residues and Phe37 was mostly interacted and bound with all of the tested HA compounds. This findings provides an opportunity for rational design of haloacid dehalogenase especially to DehE.
Effects of repeated fertilization in young Norway spruce forests

ABSTRACT Several studies have shown the positive effect of nitrogen fertilization on conifer growth. In young Norway spruce (Picea abies) stands, an additional effect of including a mixture of other nutrients has often, but not always, been found. We studied effects of repeated fertilization in 28 stands with young Norway spruce in central Norway. The treatments consisted of plots without nutrient addition (Control), fertilization with 150 kg N ha−1 (150 N), and fertilization with 150 kg N plus addition of P, K, Mg, B, Mn and Cu (150 N + mix), repeated three times with approximately eight years interval. There was a clear positive effect on volume increment of the 150 N and 150 N + mix treatments compared to Control, and the effect was significantly higher for 150 N + mix than for 150 N. Fertilization had a stronger effect in the first fertilization period than in the second, while the third period was intermediate. The effect of 150 N + mix was strongest at plots > 300 m a.s. l. However, this correlation may be due to geological conditions rather than elevation. Further studies are needed to find out under which edaphic conditions a nutrient mixture will increase growth substantially in young spruce stands.
VIRAL REGULATION OF CAP-DEPENDENT MESSENGER RNA TRANSLATION INHIBITOR 4E-BP1 DURING MITOSIS

The work described in this dissertation started in 2013 and focuses on the activation of cap-dependent mRNA translation and regulation of the translation inhibitor protein 4E-BP1 during mitosis. By investigating the viral oncoprotein Merkel cell polyomavirus small T antigen (MCV sT), an alternative pathway for cap-dependent mRNA translation regulation through the CDK1 kinase was discovered. In addition, a novel phosphorylation site of 4E-BP1—Ser83—was identified in mitotic cells, and a polyclonal antibody against this phosphorylation site was generated. The phospho-Ser83 4E-BP1 antibody is a useful tool that can be used as a bona fide mitotic marker by various assays: immunoblotting, immunofluorescence, and flow cytometry. Overall, this work provokes a reassessment of protein synthesis regulation during cell division, hints at additional undescribed functions for 4E-BP1, and suggests that certain mRNAs translated in this phase of the cell cycle may contribute to cell proliferation and tumorigenesis.
Putrescine catabolism via DAO contributes to proline and GABA accumulation in roots of lupine seedlings growing under salt stress

The levels of polyamines (PAs), proline (Pro), and γ-aminobutyric acid (GABA) as well as the activity of diamine oxidase (DAO; EC 1.4.3.6) were studied in the roots of 2-day-old lupine ( Lupinus luteus L. ‘Juno’) seedlings treated with 200 mM NaCl for 24 h. The effect of adding 1 mM aminoguanidine (AG), an inhibitor of DAO activity, was also analyzed. It was found that in roots of lupine seedlings growing under salt stress, a negative correlation between Pro accumulation and putrescine (Put) content takes place. Pro level increased in roots by about 160% and, at the same time, Put content decreased by about 60%, as a result of ca. twofold increase of DAO activity. The AG added to the seedlings almost totally inhibited the activity of DAO, increased Put accumulation to control level, decreased Pro content by about 25%, and reduced GABA level by about 22%. Addition of 50 mM GABA to the lupine seedlings growing in the presence of AG and NaCl restored Pro content in roots to its level in NaCl-treated plants. In this research, the clear correlation between Put degradation and GABA and Pro accumulation was shown for the first time in the roots of seedlings growing under salt stress. This could be considered as a short-term response of a plant to high salt concentration. Our findings indicate that during intensive Pro accumulation in roots induced by salt stress, the pool of this amino acid is indirectly supported by GABA production as a result of Put degradation.
Detection and evolutionary analysis of functional conserved non-coding sequences in higher plants by integrating evolutionary and functional conservation

In higher organisms, gene promoters and their cis-regulatory element composition play an essential role for the regulation of gene transcription. Hence, identification and functional characterization of cis-elements has become a major task for understanding the regulatory mechanisms and circuits. In this work, various complementary approaches that make use of phylogenetic approaches and/or the combination of genome and transcriptome data have been applied to address large-scale detection of cis-regulatory elements in grass species for the first time. Moreover, evolutionary analysis of novel and verified cis-elements has been undertaken in Arabidopsis linage and among five distinct platid genomes of Oenothera species. Together, a foundation on the path was laid to develop a compendium of functional elements for plants, including their compositions, evolutionary mechanisms and functions on phenotypic changes.
Enzymolysis reaction kinetics and thermodynamics of rapeseed protein with sequential dual‐frequency ultrasound pretreatment

We evaluated the effect of sequential dual-frequency ultrasound (SDFU) pretreatments on rapeseed protein enzymolysis, using alcalase as a model enzyme. Hydrolysed protein concentrations, enzymolysis kinetics and thermodynamic parameters were investigated. The results showed that the hydrolysed rapeseed protein concentration following SDFU pretreatments was higher compared to that of the control for up to 75 min of enzymolysis at various substrate concentrations of 5–25 g L ; both control and SDFU pretreatment groups showed first-order reaction kinetics. Compared to the control, the Michaelis–Menten constant (KM) value decreased remarkably by 17.61%, while an increase in the binding frequency between enzyme and substrate (KA) by 10.47% was observed. The thermodynamic parameters, enthalpy, entropy and activation energy were reduced in the SDFU pretreatment group compared to the control by 31.78%, 18.0% and 29.56%, respectively. SDFU pretreatment showed little effect on Gibbs free energy at the various temperatures studied.