Miracle-dz/UniFAR-FTUs huggingface dataset:
SEX AND SPECIATION: GENETIC ARCHITECTURE AND EVOLUTIONARY POTENTIAL OF SEXUAL VERSUS NONSEXUAL TRAITS IN THE SIBLING SPECIES OF THE DROSOPHILA MELANOGASTER COMPLEX

Phenotypic divergence in the male reproductive system (genitalia and gonads) between species of the Drosophila melanogaster complex and their hybrids was quantified to decipher the role of these traits in species differentiation and speciation. Internal as well as external, sexual and nonsexual traits were analyzed with respect to genetic variation and trait asymmetry between strains within species, genetic divergence between species, and dominance and asymmetry in species and hybrids. The variation between strains within species was significant among sexual traits, and only external traits were less asymmetric than internal ones, which suggests that sexual traits are not strongly constrained within species. Three main findings show that sexual traits are most divergent between species: (1) testis length and area, and the area of the posterior lobe of the genital arch (sexual traits) showed the highest proportion of variation between species; (2) linear discriminant functions with the highest components associated to sexual traits were better predictors of species membership; and (3) testis length and area revealed a departure from a linear relationship between members of the species group. Examination of interspecific hybrids showed that sexual traits had higher asymmetry in species hybrids than in the parental species and that sexual traits showed additivity or dominance whereas nonsexual traits showed overdominance (with the exception of malpighian tubules length). These results suggest that sexual traits have undergone more genetic changes and, as a result, tend to show higher divergence and stronger hybrid breakdown between species than nonsexual traits. We propose that sexual selection in the broad sense, affecting all aspects of sexuality, may be responsible for the diversified appearance of sexual traits among closely related species and that the genetic architecture underlying sexual traits may be more prone to disruption during the early stages of speciation.
ATRIP from TopBP1 to ATR—in vitro activation of a DNA damage checkpoint

DNA is susceptible to diverse types of damage throughout the cell cycle including cross-linking, oxidation, and adduct formation. DNA is especially prone to breaks during S phase, when non-B forms of DNA, such as hairpins or triplexes, can appear in the course of replication or extended regions of single-strand DNA (ssDNA) can arise by polymerase–helicase uncoupling. When genomic DNA is damaged, eukaryotic cells restrain their cell cycle progress while the damage is repaired. This so-called checkpoint mechanism (1), first described in the 1970s (2), is crucial for maintenance of genome integrity. In the ensuing years, genetic studies have contributed dramatically to understanding checkpoint mechanisms to the point where it is believed that most, if not all, proteins involved in the main checkpoint signaling pathways have been discovered. A central question remaining in this area is how the cell recognizes and transduces the diverse noncanonical structures of DNA into a checkpoint response. The paper by Choi et al. (3) in PNAS represents a major advance in this field, and it describes the in vitro assembly of a human checkpoint system from defined components.
Chapter 1 Autophagy in Cell Fate and Diseases

Autophagy pathway has been one of the hot topics during the last decade. From a general notion about its cellular role, autophagy becomes a more sophisticated phenomenon with significant implications in cellular homeostasis. Consequently, autophagy represents an emerging new factor in human diseases. Despite its general task, the bulk degradation of cellular constituents during starvation settings, autophagy possesses important cross talk and interrelationships with several cellular processes such as apoptosis and senescence, among others. This entire panorama gives us a complex but exciting scenario. Consequently, with the aim of encompassing the whole spectrum, in this chapter, we review three main topics: autophagy as a cellular process; autophagy in cell fate; and autophagy in disease. We discuss the emerging role of selective type of autophagy to avoid apoptosis or necrosis and the novel relationship between autophagy and senescence to understand the real extent that autophagy pathway has over cell fate. Finally, we briefly describe the current trends on autophagy in human pancreatic diseases and its role in cancer cell metab‐ olism.
Alteraciones funcionales de circuitos reflejos del tronco cerebral en pacientes parkinsonianos.

En esta Tesis Doctoral se pone de manifiesto que el reflejo de sobresalto acustico esta anormalmente reducido o incluso ausente en la paralisis supranuclear progresiva pero es normal en la atrofia multisistemica y normal o discretamente retrasado en la enfermedad de Parkinson. Por otro lado, las respuestas faciales a estimulos somestesicos perifericos registradas en el musculo orbicularis oculi estan ausentes en la paralisis supranuclear progresiva en relacion a otros parkinsonismos. La curva de recuperacion de la excitabilidad del reflejo de parpadeo esta alterada, sin embargo, de forma similar en los distintos sindromes parkinsonianos. Es otra de las conclusiones de la Tesis que el reflejo de sobresalto acustico origina una activacion de la via reticuloespinal que facilita la ejecucion de un acto motor determinado y acorta el tiempo de reaccion. Este fenomeno se demuestra en sujetos sanos y en pacientes con enfermedad de Parkinson y con atrofia multisistemica, pero no en pacientes con paralisis supranuclear progresiva. La ausencia de efecto sobre el tiempo de reaccion en estos pacientes se relaciona con el hecho de que el reflejo de sobresalto esta ausente o anormalmente reducido. La magnitud del efecto producido se modifica con las condiciones ambientales y el nivel de atencion. La preparacion para la ejecucion de un acto motor reduce la habituacion de la reaccion de sobresalto y facilita su aplicabilidad clinica. En resumen se puede decir que, en la paralisis supranuclear progresiva el reflejo palmomentoniano presenta una anormal distribucion de la respuesta en los musculos faciales; el reflejo de sobresalto esta ausente o reducido; el tiempo de reaccion no experimenta aceleracion tras un sobresalto acustico; ademas existe una alteracion de la curva de recuperacion de la excitabilidad del reflejo de parpadeo. En la enfermedad de Parkinson y en la atrofia multisistemica los hallazgos neurofisiologicos son similares tanto en lo que se refiere a las alteraciones en la recuperacion de la curva de excitabilidad del reflejo de parpadeo como al efecto producido sobre el tiempo de reaccion por un sobresalto acustico y a las respuestas faciales producidas por estimulos somestesicos perifericos. Las diferencias detectadas en el estudio neurofisiologico entre los distintos tipos de parkinsonismo pueden deberse a trastornos en la modulacion que ejercen los ganglios basales sobre el nucleo pedunculopontino y otros nucleos del tronco cerebral o bien ser la expresion de cambios estructurales especificos en circuitos reticuloespinales.
Conservative High-Order Finite-Difference Schemes for Low-Mach Number Flows

Three finite-difference algorithms are proposed to solve a low-Mach number approximation for the Navier? Stokes equations. These algorithms exhibit fourth-order spatial and second-order temporal accuracy. They are dissipation-free, and thus well suited for DNS and LES of turbulent flows. The key ingredient common to each of the methods presented is a Poisson equation with variable coefficient that is solved for the hydrodynamic pressure. This feature ensures that the velocity field is constrained correctly. It is shown that this approach is needed to avoid violation of the conservation of kinetic energy in the inviscid limit which would otherwise arise through the pressure term in the momentum equation. An existing set of finite-difference formulae for incompressible flow is generalized to handle arbitrary large density fluctuations with no violation of conservation through the non-linear convective terms. An algorithm which conserves mass, momentum, and kinetic energy fully is obtained when an approximate equation of state is used instead of the exact one. Results from a model problem are used to show both spatial and temporal convergence rates and several test cases are presented to illustrate the performance of the algorithms.
Yapılandırmacı Yaklaşım Işığında Okul Psikolojik Danışma ve Rehberlik Hizmetlerinde Yazılı Tekniklerin Kullanılması

20 yuz yilin basindan gunumuze kadar kuramsal olarak birbirinden farkli yaklasimlari benimseyen pek cok psikolojik danisman in uygulamalarinda yaratici yazma calismalari gunluk tutma otobiyografi siir veya mektup yazma gibi cesitli yazma tekniklerini kullanildiklarini gormek mumkundur Bununla birlikte yazmanin psikolojik danismada en yaygin kullanimi yapilandirmaci yaklasimlar icindedir Gunumuzun egitim anlayisi buyuk olcude yapilandirmaci yaklasimin etkisi altinda gorulmektedir Bu etkinin okullardaki psikolojik danisma ve rehberlik PDR hizmetlerine yansimasi kacinilmazdir Bu calismada terapotik bir arac olarak yazma teknikleri tanitildiktan sonra yapilandirmaci yaklasim isiginda okul PDR hizmetlerinde yazmanin kullanilmasina iliskin cesitli ornekler sunulmustur Ayrica PDR alaninda yazili etkinliklerin kullanilmasina iliskin bundan sonra yurutulecek arastirmalar ve yapilacak uygulamalar icin onerilerde bulunulmustur
Identification of periodontal pathogens in atheromatous plaques.

BACKGROUND Recent studies suggest that chronic infections including those associated with periodontitis increase the risk for coronary vascular disease (CVD) and stroke. We hypothesize that oral microorganisms including periodontal bacterial pathogens enter the blood stream during transient bacteremias where they may play a role in the development and progression of atherosclerosis leading to CVD. METHODS To test this hypothesis, 50 human specimens obtained during carotid endarterectomy were examined for the presence of Chlamydia pneumoniae, human cytomegalovirus, and bacterial 16S ribosomal RNA using specific oligonucleotide primers in polymerase chain reaction (PCR) assays. Approximately 100 ng of chromosomal DNA was extracted from each specimen and then amplified using standard conditions (30 cycles of 30 seconds at 95 degrees C, 30 seconds at 55 degrees C, and 30 seconds at 72 degrees C). Bacterial 16S rDNA was amplified using 2 synthetic oligonucleotide primers specific for eubacteria. The PCR product generated with the eubacterial primers was transferred to a charged nylon membrane and probed with digoxigenin-labeled synthetic oligonucleotides specific for Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Porphyromonas gingivalis, and Prevotella intermedia. RESULTS Eighty percent of the 50 endarterectomy specimens were positive in 1 or more of the PCR assays. Thirty-eight percent were positive for HCMV and 18% percent were positive for C. pneumoniae. PCR assays for bacterial 16S rDNA also indicated the presence of bacteria in 72% of the surgical specimens. Subsequent hybridization of the bacterial 16S rDNA positive specimens with species-specific oligonucleotide probes revealed that 44% of the 50 atheromas were positive for at least one of the target periodontal pathogens. Thirty percent of the surgical specimens were positive for B. forsythus, 26% were positive for P. gingivalis, 18% were positive for A. actinomycetemcomitans, and 14% were positive for P. intermedia. In the surgical specimens positive for periodontal pathogens, more than 1 species was most often detected. Thirteen (59%) of the 22 periodontal pathogen-positive surgical specimens were positive for 2 or more of the target species. CONCLUSIONS Periodontal pathogens are present in atherosclerotic plaques where, like other infectious microorganisms such as C. pneumoniae, they may play a role in the development and progression of atherosclerosis leading to coronary vascular disease and other clinical sequelae.
C-fos gene expression induced in cells in specific hypothalamic structures by noxious mechanical stimulation and its [correction of it's] modification by exposure of the skin to extremely high frequency irradiation.

OBJECTIVES The purpose of this study was to determine: 1) The spatial pattern of c-fos gene expression in rat hypothalamic neurons after exposure to NMS and 2) The expression of c-fos gene after combined exposure to NMS and EHF irradiation of the rat skin. METHODS The experiments were performed on 28 male adult Sprague-Dawley rats. After rats were subjected to noxious mechanical stimulation (NMS) or its combination with EHF irradiation of the skin, cells in various hypothalamic structures were analyzed to determine theirs effects on c-fos gene expression, an accepted marker of the activation of neurons. C-Fos-like protein was revealed by an indirect immunoperoxidase method. RESULTS This study revealed that NMS stimulates c-fos gene expression in the anterior hypothalamic nucleus (AHN), dorsomedial hypothalamic nucleus (DMH), ventromedial hypothalamic nucleus (VMH), and lateral hypothalamic area (LHA) by 157, 101, 199 and 115% respectively compared to control animals. Combined exposure to NMS and EHF irradiation directed at the skin in the region of the St36 acupuncture point projection site (left side) results in a decrease of the number of neurons that are activated in the AHN, DMH, VMH, and LHA by 33.6, 13.2, 31.0 and 32.9% respectively compared to the number of neurons activated by exposure to NMS by itself. EHF exposure of the skin of rats not subjected to NMS differentially effects the number of c-Fos positive cells expressed in hypothalamic structures: a decrease of 39.7% was observed in the number of activated neurons in the central part of LHA (level 28) compared to sham-irradiated animals, while an increase of 80.95% was noted in the number of c-Fos positive cells in the DMH compared to sham-irradiated animals. CONCLUSIONS The spatial pattern and degree of activation of c-fos gene expression has been shown in cells of the hypothalamus of rats after exposure to NMS by itself and after NMS combined with EHF irradiation of the skin. The "stress" reaction of cells in specific hypothalamic structures has been shown to be decreased after EHF exposure of the skin.
Closed-Loop Insulin Delivery during Pregnancy in Women with Type 1 Diabetes.

BACKGROUND In patients with type 1 diabetes who are not pregnant, closed-loop (automated) insulin delivery can provide better glycemic control than sensor-augmented pump therapy, but data are lacking on the efficacy, safety, and feasibility of closed-loop therapy during pregnancy. METHODS We performed an open-label, randomized, crossover study comparing overnight closed-loop therapy with sensor-augmented pump therapy, followed by a continuation phase in which the closed-loop system was used day and night. Sixteen pregnant women with type 1 diabetes completed 4 weeks of closed-loop pump therapy (intervention) and sensor-augmented pump therapy (control) in random order. During the continuation phase, 14 of the participants used the closed-loop system day and night until delivery. The primary outcome was the percentage of time that overnight glucose levels were within the target range (63 to 140 mg per deciliter [3.5 to 7.8 mmol per liter]). RESULTS The percentage of time that overnight glucose levels were in the target range was higher during closed-loop therapy than during control therapy (74.7% vs. 59.5%; absolute difference, 15.2 percentage points; 95% confidence interval, 6.1 to 24.2; P=0.002). The overnight mean glucose level was lower during closed-loop therapy than during control therapy (119 vs. 133 mg per deciliter [6.6 vs. 7.4 mmol per liter], P=0.009). There were no significant differences between closed-loop and control therapy in the percentage of time in which glucose levels were below the target range (1.3% and 1.9%, respectively; P=0.28), in insulin doses, or in adverse-event rates. During the continuation phase (up to 14.6 additional weeks, including antenatal hospitalizations, labor, and delivery), glucose levels were in the target range 68.7% of the time; the mean glucose level was 126 mg per deciliter (7.0 mmol per liter). No episodes of severe hypoglycemia requiring third-party assistance occurred during either phase. CONCLUSIONS Overnight closed-loop therapy resulted in better glucose control than sensor-augmented pump therapy in pregnant women with type 1 diabetes. Women receiving day-and-night closed-loop therapy maintained glycemic control during a high proportion of the time in a period that encompassed antenatal hospital admission, labor, and delivery. (Funded by the National Institute for Health Research and others; Current Controlled Trials number, ISRCTN71510001.).
Science and medicine of rowing: A review

The biology and medicine of rowing are briefly reviewed. Effort in a 2000 -m race is about 70% aerobic. Because the boat (and in some instances a cox) must be propelled, successful competitors are very tall, with a large lean mass and aerobic power. Large hearts may lead to erroneous diagnoses of a cardiomyopathy. Large respiratory minute volumes must be developed by chest muscles that are also involved in rowing. The vital capacity is typically large, and breathing becomes entrained. Expiration cannot be slowed relative to inspiration (as normally occurs at high rates of ventilation) and the limiting flow velocity may be reached, with the potential for airway collapse. Performance is strongly related to the power output at the ‘anaerobic threshold’, and lactate measures provide a guide to an appropriate intensity of endurance training. Peak blood lactate levels are higher in males (commonly 11–19 mmol·l -1 and occasionally as high as 25 mmol·l -1) than in females (9–11 mmol·l -1), probably because males .
NETWORK FORMULATION OF MULTIPLE-CRITERION PROBLEMS FOR DEVELOPING AN INTEGRATED PERSONNEL DISTRIBUTION SYSTEM IN THE NAVY

Abstract : Currently, the Navy allocates and assigns thousands of personnel to job vacancies every week. In mathematical terms, it is a large-scale, multiple- criterion optimization problem. Conventional linear programming techniques are not capable of solving this type of problem efficiently. Although the newly developed network codes may offer a plausible alternative, developing a network formulation to integrate allocation and assignment processes is complicated. A number of technical problems related to simultaneously quantifying allocation goals, assignment goals, and the assignment procedure would have to be overcome. Research is needed to derive a methodology to solve these technical problems. This report discusses the development of an approach to automate major aspects of the personnel assignment process and to integrate the personnel assignment and allocation processes. Success in implementing this integrated system would not only make the assignment process efficient but would also make distribution policy evaluation and analysis feasible.
BzdR, a Repressor That Controls the Anaerobic Catabolism of Benzoate in Azoarcus sp. CIB, Is the First Member of a New Subfamily of Transcriptional Regulators*

In this work, we have studied the transcriptional regulation of the bzd operon involved in the anaerobic catabolism of benzoate in the denitrifying Azoarcus sp. strain CIB. The transcription start site of the PN promoter running the expression of the bzd catabolic genes was identified. Gel retardation assays and PN::lacZ translational fusion experiments performed both in Azoarcus sp. CIB and Escherichia coli cells have shown that bzdR encodes a specific repressor that controls the inducible expression of the adjacent bzd catabolic operon, being the first intermediate of the catabolic pathway (i.e. benzoyl-CoA, the actual inducer molecule). This is the first report of a transcriptional repressor and a CoA-derived aromatic inducer controlling gene expression in the anaerobic catabolism of aromatic compounds. DNase I footprinting experiments revealed that BzdR protected three regions (operators) at the PN promoter. The three operators contain direct repetitions of a TGCA sequence that forms part of longer palindromic structures. In agreement with the repressor role of BzdR, operator region I spans the transcription initiation site as well as the -10 sequence for recognition of the RNA polymerase. Primary sequence analyses of BzdR showed an unusual modular organization with an N-terminal region homologous to members of the HTH-XRE family of transcriptional regulators and a C-terminal region similar to shikimate kinases. A three-dimensional model of the N-terminal and C-terminal regions of BzdR, generated by comparison with the crystal structures of the SinR regulator from Bacillus subtilis and the shikimate kinase I protein from E. coli, strongly suggests that they contain the helix-turn-helix DNA-binding motif and the benzoyl-CoA binding groove, respectively. The BzdR protein constitutes, therefore, the prototype of a new subfamily of transcriptional regulators.
PyMW-a Python Module for Parallel Master Worker Computing

We describe a general purpose master-worker parallel computation Python module called PyMW. PyMW provides a unified interface to multiple computation environments including multicore processors, networked clusters and the Berkeley Open Infrastructure for Network Computing (BOINC) software platform. PyMW is intended to support rapid development, testing and deployment of large scale master-worker style computations. It is also designed to allow easy extension to other computing environments with little change in the master-worker program. We demonstrate the effectiveness and scalability of PyMW by performing several master-worker style parallel computations on a multicore machine, a networked cluster and a BOINC project.
Autonomic innervation of reproductive organs: Analysis of the neurons whose axons project in the main penile nerve in the pelvic plexus of the rat

An understanding of the composition of the various nerves of the pelvic plexus is essential in the design of studies to explore the autonomic control of pelvic visceral tissues. As a correlate of this interest, the present study was designed to determine the composition of the main penile nerve in the pelvic plexus of the laboratory rat, an animal commonly used for studies of reproductive physiology. Retrograde tracing studies indicate that the main penile nerve contains neurons which project to the penile crura, the corpus spongiosum, and the bulbourethral glands. The main penile nerve is the major source of neurons which innervate the corpus spongiosum and bulbourethral gland and contains about one‐third of all parasympathetic neurons which project to the penile crura. Dye placed on the proximal cut end of the main penile nerve indicates that neurons in the parasympathetic region of the spinal cord (L6‐S1) and to a lesser extent a sympathetic region of the cord, L1‐L2, provide preganglionic innervation to ganglion cells in the main pelvic nerve. Processes of neurons in dorsal root ganglia L6‐S1 and of neurons in the abdominopelvic sympathetic chain course in the main penile nerve to unknown destinations. In many respects this presumed postganglionic fiber tract is essentially a region of the pelvic plexus which subserves extrapelvic visceral tissues.