Miracle-dz/UniFAR-FTUs huggingface dataset:
High Risks of Losing Genetic Diversity in an Endemic Mauritian Gecko: Implications for Conservation

Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.
Efficacy of meaning-centered group psychotherapy for cancer survivors: a randomized controlled trial

Background The aim of this study was to assess the efficacy of meaning-centered group psychotherapy for cancer survivors (MCGP-CS) to improve personal meaning, compared with supportive group psychotherapy (SGP) and care as usual (CAU). Method A total of 170 cancer survivors were randomly assigned to one of the three study arms: MCGP-CS (n = 57); SGP (n = 56); CAU (n = 57). The primary outcome measure was the Personal Meaning Profile (PMP; total score). Secondary outcome measures were subscales of the PMP, psychological well-being (Scales of Psychological Well-being; SPWB), post-traumatic growth (Posttraumatic Growth Inventory), Mental Adjustment to Cancer (MAC), optimism (Life Orientation Test-Revised), hopelessness (Beck's Hopelessness Scale), psychological distress (anxiety and depression, Hospital Anxiety and Depression Scale; HADS) and quality of life (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire; EORTC QLQ-C30). Outcome measures were assessed before randomization, post-intervention, and after 3 and 6 months of follow-up (FU). Results Linear mixed model analyses (intention-to-treat) showed significant differences between MCGP-CS, SGP and CAU on the total PMP score, and on (sub)scales of the PMP, SPWB, MAC and HADS. Post-hoc analyses showed significantly stronger treatment effects of MCGP-CS compared with CAU on personal meaning (d = 0.81), goal-orientedness (d = 1.07), positive relations (d = 0.59), purpose in life (d = 0.69); fighting spirit (d = 0.61) (post-intervention) and helpless/hopeless (d = −0.87) (3 months FU); and distress (d = −0.6) and depression (d = −0.38) (6 months FU). Significantly stronger effects of MCGP-CS compared with SGP were found on personal growth (d = 0.57) (3 months FU) and environmental mastery (d = 0.66) (6 months FU). Conclusions MCGP-CS is an effective intervention for cancer survivors to improve personal meaning, psychological well-being and mental adjustment to cancer in the short term, and to reduce psychological distress in the long run.
Fluorescence Resonance Energy Transfer-Based Intracellular Assay for the Conformation of Hepatitis C Virus Drug Target NS 5 A

Nonstructural protein 5A (NS5A) is essential for hepatitis C virus (HCV) replication and assembly and is a critical drug target. Biochemical data suggest large parts of NS5A are unfolded as an isolated protein, but little is known about its folded state in the cell. We used fluorescence resonance energy transfer (FRET) to probe whether or not different regions of NS5A are in close proximity within the cell. Twenty-three separate reporter constructs were created by inserting one or more fluorophores into different positions throughout the three domains of NS5A. FRET efficiency was maximal when donor and acceptor fluorophores were positioned next to each other but also could be observed when the two fluorophores flanked NS5A domain 1 or domain 3. Informatic and biochemical analysis suggests that large portions of the carboxy terminus of NS5A are in an unfolded and disordered state. Quercetin, a natural product known to disrupt NS5A function in cells, specifically disrupted a conformationally specific domain 3 FRET signal. Intermolecular FRET indicated that the NS5A amino termini, but not other regions, are in close proximity in multimeric complexes. Overall, this assay provides a new window on the intracellular conformation(s) of NS5A and how the conformation changes in response to cellular and viral components of the replication and assembly complex as well as antiviral drugs.
Complete Genome Sequence of the Methanococcus maripaludis Type Strain JJ (DSM 2067), a Model for Selenoprotein Synthesis in Archaea

ABSTRACT Methanococcus maripaludis type strain JJ (DSM 2067) is an important organism because it serves as a model for primary energy metabolism and hydrogenotrophic methanogenesis and is amenable to genetic manipulation. The complete genome (1.7 Mb) harbors 1,815 predicted protein-encoding genes, including 9 encoding selenoproteins.
The Increased Forming Limits of Incremental Sheet Forming Processes

Incremental sheet forming is known to give higher forming limits than conventional sheet forming processes, but investigation of this effect has been impeded by the computational cost of process models which include detailed predictions of through thickness behaviour. Here, a simplified process is used to gain insight into the mechanics of a broad class of incremental forming processes. The simplified process is described and shown to give increases in forming limits compared to a conventional process with the same geometry. A model of the process is set up with a commercial finite element package, validated, and used to trace the history of a ‘pin’ inserted perpendicularly into the workpiece. The history of the deformation of the ‘pin’ demonstrates significant through thickness shear occurring in the direction parallel to tool motion. This insight is used to modify an existing analysis used to predict forming limit curves. The analysis shows that for a sheet with uniform proportional loading, the forming limit is increased when through thickness shear is present, and this is proposed as an explanation for the increased forming limits of incremental sheet forming processes.
Approaches to the Moisture Content Monitoring Intimber Elements: Development of a Resistive Method

The scope of this work is based on the use of resistive method to quantify the water content in timber elements. For an in-depth mapping, we adapted a multiplexed technique derived from geophysics based on a maximum crossing of current lines to obtain topography of measures sweeping the space boundary conditions being defined by the sample. The calibration of these measures is completed by a gammadensimetry laboratory method which allows access to water profiles along a preferred direction. Nevertheless, the resistive method is penalized by logarithmic laws linking moisture and resistivity. So, we develop a hybrid method for coupling the data obtained to diffusion models: it will provide complementary information where resistivity and gammadensimetry are no longer effective. The developed experimental protocol allows employing the selected method and optimizing the diffusion properties (diffusion coefficient and convective exchange coefficient) injected into a characterization algorithm (Nelder-Mead’s simplex inversion method) based on a finite difference method for the Fick’s diffusion law determination integrating orthotropic and non- linear properties. Overlap between electric field and density measurements and the numerical simulation tool are possible.
Understanding and Treating Supralevator Fistula-in-Ano: MRI Analysis of 51 Cases and a Review of Literature

BACKGROUND: Supralevator fistulas are highly complex. The delineation of the supralevator fistula has become accurate because of MRI. OBJECTIVE: The aim of the study was to analyze the pathophysiology and treatment of different types of supralevator fistulas. DESIGN: This was a prospective study. SETTINGS: The study was conducted at a specialized fistula treatment center in North India. PATIENTS: All of the patients with fistula-in-ano who presented in the outpatient department were assessed with a physical examination and MRI scan. The patients in whom the supralevator extension was confirmed on MRI were included in the study. MAIN OUTCOME MEASURES: The MRI scans of patients included in the study were analyzed in detail to assess the types of supralevator fistulas and other characteristics of these fistulas. The patients who were operated on were followed for cure rate and deterioration in incontinence. RESULTS: Of 702 patients with fistula-in-ano who were analyzed by MRI over a period of 3 years, 51 patients with supralevator fistula-in-ano were identified. The mean age was 44.3 ± 12.1 years and the male:female ratio was 16:1. The incidence of supralevator fistulas was 7.26% (51 of 702). In supralevator fistulas, the supralevator extension (upper part) was found to be in the intersphincteric plane in all of the patients. This upper part could be successfully managed by laying it open through the transanal route. The infralevator (lower) part could be of 3 types: intersphincteric (n = 13), low transsphincteric (n = 3), or high transsphincteric (n = 35). The lower part could be managed conventionally. There were no extrasphincteric fistulas. An extensive review of the literature revealed only 2 studies (total fistulas = 16) in which supralevator fistula was studied. LIMITATIONS: This was a retrospective study. CONCLUSIONS: The upper supralevator extension in all of the supralevator fistulas is almost always in the intersphincteric plane. This upper part could be laid open through the transanal route. The lower infralevator part could be of 3 types, intersphincteric, low transsphincteric, or high transsphincteric, which could be managed conventionally. Thus, supralevator fistulas could be managed successfully and easily. See Video Abstract at http://links.lww. com/DCR/A630.
Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I

Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction. These two activities are tightly regulated to prevent over-methylation or auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All high-resolution structures of C-protein/DNA-protein complexes solved to date relate to C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or the phosphate backbone could be observed. Here we present both structural and DNA binding data for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding affinity than mutations to those residues that bind directly to the bases (T36, R46), and the contributions of each side chain to the binding energies are compared. High-resolution X-ray crystal structures of the mutant and native proteins showed that the fold of the proteins was unaffected by the mutations, but also revealed variation in the flexible loop conformations associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA complex by X-ray crystallography to allow us to directly compare the structure of the DNA in the mutant and native complexes.
Infectious rabies viruses from cloned cDNA.

The generation of infectious rabies virus (RV), a non‐segmented negative‐stranded RNA virus of the Rhabdoviridae family, entirely from cloned cDNA is described. Simultaneous intracellular expression of genetically marked full‐length RV antigenome‐like T7 RNA polymerase transcripts and RV N, P and L proteins from transfected plasmids resulted in formation of transcriptionally active nucleocapsids and subsequent assembly and budding of infectious rabies virions. In addition to authentic RV, two novel infectious RVs characterized by predicted transcription patterns were recovered from modified cDNA. Deletion of the entire non‐translated pseudogene region, which is conserved in all naturally occurring RVs, did not impair propagation of the resulting virus in cell culture. This indicates that non‐essential genetic material might be present in the genomes of non‐segmented RNA viruses. The introduction of a functional extra cistron border into the genome of another virus resulted in the transcription of an additional polyadenylated mRNA containing pseudogene sequences. The possibility of manipulating the RV genome by recombinant DNA techniques using the described procedure‐‐potentially applicable also for other negative‐stranded viruses‐‐greatly facilitates the investigation of RV genetics, virus‐host interactions and rabies pathogenesis and provides a tool for the design of new generations of live vaccines.
Gaze Duration Biases for Colours in Combination with Dissonant and Consonant Sounds: A Comparative Eye-Tracking Study with Orangutans

Research on colour preferences in humans and non-human primates suggests similar patterns of biases for and avoidance of specific colours, indicating that these colours are connected to a psychological reaction. Similarly, in the acoustic domain, approach reactions to consonant sounds (considered as positive) and avoidance reactions to dissonant sounds (considered as negative) have been found in human adults and children, and it has been demonstrated that non-human primates are able to discriminate between consonant and dissonant sounds. Yet it remains unclear whether the visual and acoustic approach–avoidance patterns remain consistent when both types of stimuli are combined, how they relate to and influence each other, and whether these are similar for humans and other primates. Therefore, to investigate whether gaze duration biases for colours are similar across primates and whether reactions to consonant and dissonant sounds cumulate with reactions to specific colours, we conducted an eye-tracking study in which we compared humans with one species of great apes, the orangutans. We presented four different colours either in isolation or in combination with consonant and dissonant sounds. We hypothesised that the viewing time for specific colours should be influenced by dissonant sounds and that previously existing avoidance behaviours with regard to colours should be intensified, reflecting their association with negative acoustic information. The results showed that the humans had constant gaze durations which were independent of the auditory stimulus, with a clear avoidance of yellow. In contrast, the orangutans did not show any clear gaze duration bias or avoidance of colours, and they were also not influenced by the auditory stimuli. In conclusion, our findings only partially support the previously identified pattern of biases for and avoidance of specific colours in humans and do not confirm such a pattern for orangutans.
MicroRNA signatures characterize diffuse large B‐cell lymphomas and follicular lymphomas

MicroRNAs (miRNA, miR) are negative regulators of gene expression that play an important role in diverse biological processes such as development, cell growth, apoptosis and haematopoiesis, suggesting their association with cancer. Here we analysed the expression signatures of 157 miRNAs in 58 diffuse large B‐cell lymphoma (DLBCL), 46 follicular lymphoma (FL) and seven non‐neoplastic lymph nodes (LN). Comparison of the possible combinations of DLBCL‐, FL‐ and LN resulted in specific DLBCL‐ and FL‐signatures, which include miRNAs with previously published function in haematopoiesis (MIRN150 and MIRN155) or tumour development (MIRN210, MIRN10A, MIRN17‐5P and MIRN145). As compared to LN, some miRNAs are differentially regulated in both lymphoma types (MIRN155, MIRN210, MIRN106A, MIRN149 and MIRN139). Conversely, some miRNAs show lymphoma‐specific aberrant expression, such as MIRN9/9*, MIRN301, MIRN338 and MIRN213 in FL and MIRN150, MIRN17‐5P, MIRN145, MIRN328 and others in DLBCL. A classification tree was computed using four miRNAs (MIRN330, MIRN17‐5P, MIRN106a and MIRN210) to correctly identify 98% of all 111 cases that were analysed in this study. Finally, eight miRNAs were found to correlate with event‐free and overall survival in DLBCL including known tumour suppressors (MIRN21, MIRN127 and MIRN34a) and oncogenes (MIRN195 and MIRNLET7G).
Micro- and Nanotextured Silicon for Antireflective Coatings of Solar Cells

The paper deals with obtaining of textured silicon surfaces by chemical etching. As a result of experiments based on the modification and optimization of obtaining a textured silicon, several methods of chemical texturing of the crystalline silicon surface were developed. It was shown that modified isotropic and anisotropic etching methods are applicable to create a microrelief on the surface of silicon substrate. These methods in addition to their high conversion efficiency can be used for both mono- and multicrystalline silicon which would ensure their industrial use.
Fear of Hypoglycemia in the Parents of Children and Adolescents With Diabetes: Maladaptive or Healthy Response?

Sixty-one parents of children with insulin-dependent diabetes mellitus completed modified versions of the Hypoglycemic Fear Survey (HFS) and the Diabetes Quality of Life (DQOL) scale. They also indicated their child's history ofhypoglycemic related seizures or loss of consciousness (SLC) events. Parental HFS scores were significantly greater if their child had ever experienced a SLC event or experienced a SLC event within the past year. Parental HFS scores were positively correlated with general parental worry about their child having diabetes. Adolescent children who experienced a SLC event during the past year reported greater HFS scores, greater general worry about diabetes, and a greater negative impact of having diabetes compared with adolescents with no such history. Despite the greater fear of hypoglycemia in prrrents and adolescents, there was no significant difference in HbA 1 values between children with or without any history of SLC events or children with or without a SLC event within the past year.
Aging Well Among Women Veterans Compared With Non-Veterans in the Women's Health Initiative.

PURPOSE OF THE STUDY To examine whether Veteran status influences (a) women's survival to age 80 years without disease and disability and (b) indicators of successful, effective, and optimal aging at ages 80 years and older. DESIGN AND METHODS The Women's Health Initiative (WHI) enrolled 161,808 postmenopausal women aged 50-79 years from 1993 to 1998. We compared successful aging indicators collected in 2011-2012 via mailed questionnaire among 33,565 women (921 Veterans) who reached the age of 80 years and older, according to Veteran status. A second analysis focused on women with intact mobility at baseline who could have reached age 80 years by December 2013. Multinominal logistic models examined Veteran status in relation to survival to age 80 years without major disease or mobility disability versus having prevalent or incident disease, having mobility disability, or dying prior to age 80 years. RESULTS Women Veterans aged 80 years and older reported significantly lower perceived health, physical function, life satisfaction, social support, quality of life, and purpose in life scale scores compared with non-Veterans. The largest difference was in physical function scores (53.0 for Veterans vs 59.5 for non-Veterans; p < .001). Women Veterans were significantly more likely to die prior to age 80 years than non-Veteran WHI participants (multivariate adjusted odds ratio = 1.20; 95% confidence interval, 1.04-1.38). In both Veteran and non-Veteran women, healthy survival was associated with not smoking, higher physical activity, healthy body weight, and fewer depressive symptoms. IMPLICATIONS Intervening upon smoking, low physical activity, obesity, and depressive symptoms has potential to improve chances for healthy survival in older women including Veterans.
Bacteriophage applications as biocontrol agent in food packaging materials

Bacteriophages or phages are the most prevalent organisms in the world and spread widely in different species of food. The most promising system is the use of bacteriophages against pathogenic bacteria in food for biocontrol. In order to provide biocontrol in an effective manner, it is necessary to determine the host phage by control of bacteriophages for each pathogen species. Nowadays, researchers are focusing on foodborne pathogenic bacteria such as Campylobacter jejuni, E. coli O157: H7, Listeria monocytogenes and Salmonella spp. In recent years, several studies have been carried out with the aim of developing new packaging films with antimicrobial properties and the use of bacteriophages with antimicrobial properties in active packaging formulations is an outstanding research topic. To expand the use of phages beyond direct spraying of phages on food products, there is a need to develop material formulations that can encapsulate phages for improved stability and release at target sites for delivery. Thus, phages can have significant applications as additives to packaging material formulations. In this chapter, the antimicrobial properties of bacteriophages and their potential for use in food packaging materials will be discussed with potential applications of their advantages and disadvantages.