Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating gene expression and codon specific translational efficiencies, mutation biases, and selection coefficients from genomic data alone

Extracting biologically meaningful information from the continuing flood of genomic data is a major challenge in the life sciences. Codon usage bias (CUB) is a general feature of most genomes and is thought to reflect the effects of both natural selection for efficient translation and mutation bias. Here we present a mechanistically interpretable, Bayesian model (ROC SEMPPR) to extract biologically meaningful information from patterns of CUB within a genome. ROC SEMPPR, is grounded in population genetics and allows us to separate the contributions of mutational biases and natural selection against translational inefficiency on a gene by gene and codon by codon basis. Until now, the primary disadvantage of similar approaches was the need for genome scale measurements of gene expression. Here we demonstrate that it is possible to both extract accurate estimates of codon specific mutation biases and translational efficiencies while simultaneously generating accurate estimates of gene expression, rather than requiring such information. We demonstrate the utility of ROC SEMPPR using the S. cerevisiae S288c genome. When we compare our model fits with previous approaches we observe an exceptionally high agreement between estimates of both codon specific parameters and gene expression levels (ρ > 0.99 in all cases). We also observe strong agreement between our parameter estimates and those derived from alternative datasets. For example, our estimates of mutation bias and those from mutational accumulation exper-iments are highly correlated (ρ = 0.95). Our estimates of codon specific translational inefficiencies are tRNA copy number based estimates of ribosome pausing time (ρ = 0.64), and mRNA and ribosome profiling footprint based estimates of gene expression (ρ = 0.53 − 0.74) are also highly correlated, thus supporting the hypothesis that selection against translational inefficiency is an important force driving the evolution of CUB. Surprisingly, we find that for particular amino acids, codon usage in highly expressed genes can still be largely driven by mutation bias and that failing to take mutation bias into account can lead to the misidentification of an amino acid’s ‘optimal’ codon. In conclusion, our method demonstrates that an enormous amount of biologically important information is encoded within genome scale patterns of codon usage, accessing this information does not require gene expression measurements, but instead carefully formulated biologically interpretable models.
New techniques for automatic speaker verification

An interactive automatic speaker verification system has been augmented to include linear prediction parameters in addition to the already existing pitch and intensity analysis of sentence-long utterances. This improved system has been evaluated on a new and enlarged speaker population. A method for selecting optimum speaker-dependent features has been incorporated in this system which significantly improves its performance. The evaluation indicates that verification error rate is approximately 1 percent with respect to casual impostors and 4 percent with respect to well-trained mimics.
Biochemistry & Molecular Biology of Plants

Since its publication in 2000, Biochemistry & Molecular Biology of Plants, has been hailed as a major contribution to the plant sciences literature and critical acclaim has been matched by global sales success. Maintaining the scope and focus of the first edition, the second will provide a major update, include much new material and reorganise some chapters to further improve the presentation. This book is meticulously organised and richly illustrated, having over 1,000 full-colour illustrations and 500 photographs. It is divided into five parts covering: Compartments: Cell Reproduction: Energy Flow; Metabolic and Developmental Integration; and Plant Environment and Agriculture. Specific changes to this edition include: Completely revised with over half of the chapters having a major rewrite. Includes two new chapters on signal transduction and responses to pathogens. Restructuring of section on cell reproduction for improved presentation. Dedicated website to include all illustrative material. Biochemistry & Molecular Biology of Plants holds a unique place in the plant sciences literature as it provides the only comprehensive, authoritative, integrated single volume book in this essential field of study.
Avaliação nutricional do milho com maior teor de óleo, nas formas de grãos secos e silagens, para suínos nas fases de crescimento e terminação

ABSTRACT - Two experiments were carried out to determine nutritive value and verify performance of growing andfinishing swine feed high moisture corn silage (HMCS) and reconstituted silage (RS) of higher oil corn. The digestibility assaywas carried twelve cross breed barrow, were allotted in metabolism cages, in a completely randomized design. The values ofdigestible dry matter (DDM), digestible protein (DP), digestible starch (DS), digestible ether extract (DEE), digestible organicmatter (DOM), digestible energy (DE) and metabolizable energy (ME) were for DG, HMCS and RS; 83.42, 7.54, 63.90, 4.40,82.28%; 3,587 and 3,513 kcal/kg; 60.80, 4.85, 45.01, 3.10, 59.50%; 2,647 and 2,509 kcal/kg; 66.48, 6.16, 49.04, 3.41, 65.67%;2,853 and 2,797 kcal/kg, respectively, based on natural matter. In the performance experiment thirty-two cross breed swinewere distributed in four treatments in a completely randomized design, with four experimental units and two pigs per experimentalunits. The treatments consisted of a basal corn and soybean meal diet and three diets with total replacement of common cornby DG, HMCS and RS higher oil corn based on the digestible energy. No differences were found among the treatments in the growin gphase. In finishing phase, daily feed intake increased for the HMCS when compared with the control diet. The price of the dietper kilogram gain of body weight for the HMCS had decreased, in growing phase and finishing phase. It was concluded that theDG, HMCS and RS, could totally replace the common corn on growing and finishing diet, without impairing performance. Dietswith high moisture corn silage resulted in smaller cost per kilogram of produced animal.Key Words: carcass traits, digestibility, energy values, performance
THE ETHIOPIAN WATER MOUSE NILOPEGAMYS OSGOOD, WITH COMMENTS ON SEMI-AQUATIC ADAPTATIONS IN AFRICAN MURIDAE

Abstract A highly distinctive rodent from the highlands of Ethiopia is currently being confused with a very different mouse from the Zaire Basin. The Ethiopian water mouse, Nilopegamys Osgood 1928, can be distinguished from Colomys and all other African murids by external, cranial, post-cranial and dental characters. Adaptations of Nilopegamys for swimming are more extreme than those of any other African murid; as noted by Osgood, it is the only one with specializations reminiscent of Neotropical ichthyomyines or Australasian hydromyines. However, the African mice Colomys, Malacomys, and Deomys also exhibit varying degrees of semi-aquatic specializations. These genera constitute a previously unrecognized guild of ‘waders’. Without swimming and while perched on elongate hind feet, all three consume insects and other small animals in shallow forest streams and pools. Both waders and swimmers show neurological adaptations to life in water, but Nilopegamys redefines certain extremes of cerebral development among African murids. Resurrected from synonymy with Colomys, this genus further accentuates the distinctiveness and imperilled status of the Ethiopian highland fauna.
Atlas of the Open Reading Frames in Human Diseases: Dark Matter of the Human Genome

Background: The human genome encodes RNA and protein coding sequences, the non-coding RNAs, pseudogenes and uncharacterized Open Reading Frames (ORFs). The dark matter of the human genome encompassing the uncharacterized proteins and the non-coding RNAs are least well studied. However, they offer novel druggable targets and biomarkers discovery for diverse diseases. Methods: In this study, we have systematically dissected the dark matter of the human genome. Using diverse bioinformatics tools, an atlas of the dark matter of the genome was created. The ORFs were characterized for gene ontology, mRNA and protein expression, protein motif and domains and genome-wide association. Results: An atlas of disease-related ORFs (n=800) was generated. A complex landscape of involvement in multiple diseases was seen for these ORFs. Motif and domains analysis
The Fundamental Theory of True 3D Virtual Reality and The Development of Scene Structure Research

Virtual reality is a reality of virtual, which can be divided into several objects and should be classified to data processing. Computer system is composed of different software and hardware, calling for the object category of real world should be entered into the corresponding computer system. In order to make calculation results presenting in the display system and realize man-machine communication, display system and computer must be matched completely. Finally, people should have an integrated control of the above system, that is to say the conversation between the user and the virtual scene. This process can be expressed with mathematical formula as follows: Setting World as virtual reality world, this can be divided into different sub object W (W1, W2, W3. (Wn); M is a computer system M (M1, M2, M3. Mn); Q is the display system Q (Q1, Q2, Q3. Qn). Defining the virtual scene which needs to be built: Watch: World →W (W1, W2, W3. Wn) Introducing the classification of virtual worlds into the computer system and defining the input function as f (x): f(x): W → f(M) Projecting the computer processing results onto the display system and defining the performance function as S (y): S (y): F (M) → S (Q) As for conservation between human and virtual scene dialog, defining the control function as A (Z): A (z): S (Q) * M + Z, (Z : human factor) [World, W, M, Q, Watch, f (x), S (y), A (z)] constitute the theoretical framework of virtual reality. In the essential process of F(x) function operation, the important content is modeling the virtual scene, which refers to geometric modeling, motion modeling and physical modeling.
Parvalbumine et régulation du transport ionique dans le tube contourné distal du rein.

Chaque jour, nos reins filtrent environ 180 litres de plasma et reabsorbent plus de 99 % du sodium filtre, ce qui correspond a plus d’un kilogramme de sel (NaCl). Cette reabsorption massive de NaCl depend de mecanismes operant dans les cellules epitheliales bordant divers segments tubulaires specialises au niveau du nephron [1]. Ainsi, les cellules du tube proximal du rein reabsorbent les deux tiers environ de la charge filtree, alors que les segments plus distaux du nephron - portion epaisse ascendante de l’anse de Henle (TAL, thick ascending limb) et tube contourne distal (TCD) - sont responsables de la reabsorption de 25 % et de 5 a 10 % du NaCl filtre, respectivement. La reabsorption de NaCl dans ces deux segments peut etre inhibee par des agents diuretiques. Les diuretiques agissant au niveau de l’anse (furosemide, bumetanide), qui bloquent le cotransporteur Na+-K+-2Cl- (NKCC2) au niveau du TAL, sont de puissants agents utilises pour traiter la retention hydrosaline, alors que les derives thiazidiques (hydrochlorothiazide, bendroflumethiazide, indapamide…), qui bloquent le cotransporteur Na+-Cl- (NCC) au niveau du TCD, sont largement utilises dans le traitement de l’hypertension arterielle.
Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?

The idea that aging follows a predetermined sequence of events, a program, has been discredited by most contemporary authors. Instead, aging is largely thought to occur due to the accumulation of various forms of molecular damage. Recent work employing functional genomics now suggests that, indeed, certain facets of mammalian aging may follow predetermined patterns encoded in the genome as part of developmental processes. It appears that genetic programs coordinating some aspects of growth and development persist into adulthood and may become detrimental. This link between development and aging may occur due to regulated processes, including through the action of microRNAs and epigenetic mechanisms. Taken together with other results, in particular from worms, these findings provide evidence that some aging changes are not primarily a result of a build-up of stochastic damage but are rather a product of regulated processes. These processes are interpreted as forms of antagonistic pleiotropy, the product of a “shortsighted watchmaker,” and thus do not assume aging evolved for a purpose. Overall, it appears that the genome does, indeed, contain specific instructions that drive aging in animals, a radical shift in our perception of the aging process. —de Magalhães, J. P. Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?
How Telomeres Solve the End-Protection Problem

The ends of eukaryotic chromosomes have the potential to be mistaken for damaged or broken DNA and must therefore be protected from cellular DNA damage response pathways. Otherwise, cells might permanently arrest in the cell cycle, and attempts to “repair” the chromosome ends would have devastating consequences for genome integrity. This end-protection problem is solved by protein-DNA complexes called telomeres. Studies of mammalian cells have recently uncovered the mechanism by which telomeres disguise the chromosome ends. Comparison to unicellular eukaryotes reveals key differences in the DNA damage response systems that inadvertently threaten chromosome ends. Telomeres appear to be tailored to these variations, explaining their variable structure and composition.
Comparative study of safety and efficacy of oral betamethasone pulse therapy and azathioprine in vitiligo

Background: Vitiligo is a common skin disorder causing depigmented macules that can impair a patient's quality of life. There are number of treatment modalities are available but at the present, there are no studies compairing betamethasone pulse therapy versus azathioprine daily therapy in treatment of vitiligo. Objectives: To compare the safety and efficacy of Azathioprine daily and Betamethasone pulse therapy in the treatment of in vitiligo. Materials and Methods: We included two vitiligo patient groups. namely group A and group B Patients of group A were given oral Azathioprine to be given 50mg twice daily and those of second group B, Betamethasone were given as a single oral dose of 5 mg on two consecutive days per week. Therapy in both groups was given for a total of 6months with follow up at 1, 3 and 6th month. Clinical photographs were taken at each visit. Side-effects if any were noted. Results were calculated with help of VASI score (vitiligo area severity index). Results: At the baseline: The patients to group A (SD 3.81± 2.3) and of group B (SD 3.76± 2.28) were having depigmented patches (P = 0.90). At the first follow up: Although there was significant improvement with perifollicular repigmentation started in both groups but the patients are of group B (SD 3.38±2.06) were showing slower response as compared to oral group A (SD 3.70± 2.28). At the second follow up: Remarkable improvement is seen in both groups compared (P = 0.17). At the third follow up: Significant improvement is seen in both groups compared (P = 0.09). Conclusions: Azathioprine and betamethasone pulse therapy are equally effective in treatment of vitiligo.
Facial asymmetry in slavic populations: Sex dimorphism in healthy young ukrainians

Introduction: Facial and body asymmetry to some extent is present in all individuals. Because fluctuating asymmetry is of a stochastic nature, it cannot be studied at the level of individuals, but only its groups can be considering during studying the populations. Material and Methods: We conducted a survey of 200 students of 8–11 grades, from 13 to 17 years old, residents of Ukraine. Asymmetry measurements were made in the program GIMP-2.8. Results: Population distribution of eight points of the face asymmetry among the population of Ukraine was studied. Sex dimorphism was found under all average indicators of absolute and relative asymmetry. Higher indicators of asymmetry were common to males and also typical for the lower part of the face. Discussion and Conclusion: Obtained data complement the existing study on facial asymmetry in human. Some of our results are consistent with the existing data from previous studies of the world population, while others point to the differences of Slavic population in a number of features related to the facial asymmetry.
Theories of Human Aging of Molecules to Society

Aging is a process of deterioration of physiological functions, time-dependent, leading to homeoestenosis. The causes and mechanisms of this process are not yet fully clarified so have issued numerous theories to explain it.The article reviews the major theories of human aging, while proposing a classification that covers the fundamental mechanisms, including deregulation of the immune response (oxy-inflamm-aging) as one of the most cited today.The theories also include those relating to the psychosocial aspects of aging, taking a holistic approach to this biological process of humans.
The influence of photoperiod on size and development of ovarioles in insecticide resistant and susceptible strains of the house fly Musca domestica L. (Diptera: Muscidae)

Th e ovariole development of laboratory-reared insecticide resistant and sensitive strains of the house fl y, Musca domestica L. (Diptera: Muscidae) under diff erent photoperiod regimes was examined. Flies were reared under laboratory conditions of 75 ± 5% RH, 25 ± 1 °C and 0:24, 6:18, 12:12, and 18:6 h L:D photoperiods. Each day, 20 female fl ies were collected from a cohort of females that had emerged on the same date. Ovarioles were dissected from the collected adults and microscopically examined to determine overall length and developmental stage. For the resistant strain, development was most rapid under the photoperiod regimes with more hours of darkness and steadily decreased with increasing hours of light. However, development of the susceptible strain was most rapid at both photoperiod extremes of 0:24 and 18:6 h L:D. Results also showed that the eff ect of both photoperiod and resistance status and the interaction between these factors had a signifi cant eff ect on ovariole development.
Molecular Analysis of Non-Transfusion Dependent Thalassemia Associated with Hemoglobin E-β-Thalassemia Disease without α-Thalassemia

Background The finding of many Thai Hb E-β0-thalassemia patients with non-transfusion dependent thalassemia (NTDT) phenotype without co-inheritance of α-thalassemia has prompted us to investigate the existence of other genetic modifying factors. Methods Study was done on 122 adult Thai patients with NTDT Hb E-β-thalassemia patients without co-inheritance of α-thalassemia. Multiple single-nucleotide polymorphisms (SNPs) associated with γ-globin gene expression including the Gγ-XmnI of HBG2 gene, rs2297339, rs4895441, and rs9399137 of the HBS1L-MYB gene, rs4671393 in the BCL11A gene, and G176AfsX179, T334R, R238H and −154 (C-T) in the KLF1 gene were investigated using PCR and related techniques. Results Heterozygous and homozygous for Gγ-XmnI of HBG2 gene were detected at 70.5% and 7.4%, respectively. Further DNA analysis identified the rs2297339 (C-T), rs4895441 (A-G), and rs9399137 (T-C) of HBS1L-MYB gene in 86.9%, 25.4%, and 23.0%, respectively. The rs4671393 (G-A) of the BCL11A gene was found at 31.2%. For the KLF1 gene, only T334R was detected at 9.0%. Conclusions It was found that these SNPs, when analyzed in combination, could explain the mild phenotypic expression of all cases. These results underline the importance of these informative SNPs on phenotypic expression of Hb E-β-thalassemia patients.
Genetic characterization of two vancomycin-resistant Staphylococcus aureus isolates in Kerman, Iran

Aim The aim of this study was the genetic characterization of two clinical vancomycin-resistant Staphylococcus aureus (VRSA) isolates. Materials and methods Resistance to vancomycin was determined by phenotypic method. PCR was used for detection of mecA, vanA, ermA, ermB, ermC, msrA/B, aph(2”)-Ic, aph(3ʹ)-IIIa, pvl, Immune Evasion Cluster [sea, sep, chip, sak and scn] genes and biofilm operon icaABCD. On the other hand, multilocus sequence typing and agr typing methods were performed for the determination of clonal relationship and van operon was detected and sequenced. Results Vancomycin-resistant Staphylococcus aureus strain 1 (VRSA-1) was positive for vanA, ermA, ermC, aph(2”)-Ic, aph(3ʹ)-IIIa, sea, sep, icaD genes, belonging to agr type I; SCCmec type III; spa type t030; and ST239. However, the genetic characterization of Vancomycin-resistant Staphylococcus aureus strain 2 (VRSA-2) revealed the presence of various types of resistance genes vanA, ermA, ermC, aph(2”)-Ic, aph(3ʹ)-IIIa, sea, icaD, relating to agr type I; SCCmec type III; spa type t459; and ST239. The presence of transposon Tn1546 was determined by PCR sequencing.The Basic Local Alignment Search Tool analysis of van operon in the VRSA isolates showed 99.6% sequence homology to Tn1546 in vancomycin-resistant enterococci, indicating the vanA operon has an enterococcal origin. Conclusion In conclusion, the ST239 is one of the most common clones of MRSA isolates which involved the hospital-associated infections, therefore, the emergence of VRSA isolates with ST239 increased the spread of resistance to vancomycin in the hospital settings.
Facilitation of activities for people with dementia in day care: a qualitative study exploring the experiences of staff

Background: Day care service (day care) is recommended as an activity service for home-dwelling people with dementia in Norway. However, there is limited knowledge about strategies to promote engagement and participation in activities at day care. The aim of this study was to gain understanding of the staff’s experiences on how to enhance engagement and participation in activities for attendees. Methods: The study has a qualitative design, using group interviews with staff and field observations at day care designed for people with dementia. Thematic content analysis was used to analyze interviews, and the findings from the observations were used to illuminate the findings in the interviews. Three group interviews including a total of 10 staff participants were conducted. Additionally, 35 attendees were observed during 2 days of field observations at each day care. Results: The main theme that emerged from the analysis was the staff’s primary objective to make meaningful days for the attendees. To achieve this, the importance of having individual knowledge about the attendees to enhance relationships, creating a balanced group composition, personal competence and skills of the staff, and the importance of using activities in different ways, was highlighted. Most findings from the field observations coincide with those in the interviews. However, the observations revealed that the staff seemed to have insufficient knowledge of offering individual tailored and structured meaningful activities to the attendees. There is a potential of including the attendees even more in the ongoing activities. Conclusion: Staff play an important role in promoting and facilitating activities to increase engagement and participation in activities. There is a potential for greater structured use of activities and cognitive stimulation. To avoid occupational injustice and the risk of decreased health and well-being among home-dwelling people with dementia, more differentiated and individual tailored services are needed.