Miracle-dz/UniFAR-FTUs huggingface dataset:
Sleep and Wakefulness inDrosophila melanogaster

Sleep is present and tightly regulated in every vertebrate species in which it has been carefully investigated, but what sleep is for remains a mystery. Sleep is also present in invertebrates, and an extensive analysis in Drosophila melanogaster has shown that sleep in fruit flies shows most of the fundamental features that characterize sleep in mammals. In Drosophila, sleep consists of sustained periods of quiescence associated with an increased arousal threshold. Fly sleep is modulated by several of the same stimulants and hypnotics that affect mammalian sleep. Moreover, like in mammals, fly sleep shows remarkable interindividual variability. The expression of several genes involved in energy metabolism, synaptic plasticity, and the response to cellular stress varies in Drosophila between sleep and wakefulness, and the same occurs in rodents. Brain activity also changes in flies as a function of behavioral state. Furthermore, Drosophila sleep is tightly regulated in a circadian and homeostatic manner, and the homeostatic regulation is largely independent of the circadian regulation. After sleep deprivation, recovery sleep in flies is longer in duration and more consolidated, indicated by an increase in arousal threshold and fewer brief awakenings. Finally, sleep deprivation in flies impairs vigilance and performance. Because of the extensive similarities between flies and mammals, Drosophila is now being used as a promising model system for the genetic dissection of sleep. Over the last few years, mutagenesis screens have isolated several short sleeping mutants, a demonstration that single genes can have a powerful effect on a complex trait like sleep.
Narrow endemics on coastal plains: Miocene divergence of the critically endangered genus Avellara (Compositae).

Critically endangered species representing ancient, evolutionarily isolated lineages must be given priority when allocating resources for conservation projects. Sound phylogenetic analyses and divergence time estimations are required to detect them, and studies on their population genetics, ecological requirements and breeding system are needed to understand their evolutionary history and to design efficient conservation strategies. Here we present the paradigmatic case of Avellara, a critically endangered monotypic genus of Compositae inhabiting a few swamps in the west-southwest Iberian coastal plains. Our phylogenetic and dating analyses based on nuclear (ITS) and plastid (matK) DNA sequences support a Miocene (>8.6 Ma) divergence between Avellara and closely related genera, resulting in marked morphological and ecological differentiation. We found alarmingly low levels of genetic diversity, based on AFLPs and plastid DNA sequences, and confirmed the prevalence of clonal reproduction. Species distribution modelling suggested a large macroclimatically suitable area for Avellara in the western Iberian Peninsula, but its apparently narrow microecological requirements restrict its distribution to peatlands with low-mineralised waters. Although five populations have been recorded from Spain and Portugal in the past, its current distribution may be reduced to only one population, recurrently found in the last decade but threatened by herbivory and habitat degradation. All this confirms the consideration of Avellara as a threatened species with high phylogenetic singularity, and makes it a flagship species for plant conservation in both Spain and Portugal that should be given priority in the design of in situ and ex situ conservation programmes.
Newborn hearing screening programme outcomes in a research hospital from Turkey.

BACKGROUND Universal neonatal hearing screening programmes are encouraged to define and manage hearing loss in early ages of life. The aim of this study is to introduce our 14-month three-step hearing screening programme results with 16 975 births in Turkey. METHODS In healthy neonates, Transient Evoked Otoacoustic Emission (TEOAE) is served as the initial screening in the first day of life. In newborns that did not meet pass criteria TEOAE was repeated in 10-day period. If the second test was 'refer' again, the screening was completed with auditory brainstem response (ABR). Additionally, ABR was performed for the neonates with neonatal intensive care unit (NICU) requirement and at high audiologic risk. Neonates who failed the screening test with ABR were referred for further evaluation. RESULTS A total of 15 323 newborns and 1652 NICU infants were tested. The screening coverage was 94.4%; 14 521 neonates (94.7%) passed the first screening step (TEOAE), while 802 (5.2%) neonate failed. In total, 322 (40.1%) of the neonates out of 802 was subjected to the second TEOAE after 10 days have failed and ABR was applied. From the neonates participated the third step (ABR) totalling 1974, 43 (2.17%) of neonates obtained a 'refer' response. Out of these 43 neonates, 17 neonates were (39.5%) NICU infants. From the 43 neonates, 38 cases (88.4%) were found to have hearing impairment. The false-positive rate for first step screening with TEOAE was 4.9%; second step with TEOAE was 1.85% and for ABR was 0.25%. CONCLUSIONS It is apparent that three step national hearing screening programme which has been applied for the latest years in Turkey is an accurate and non-invasive method to determine the congenital hearing loss. In the future, screening programmes could be rearranged with two steps as initial with TEOAE and retest with ABR and the coverage of the screening programme can be extended.
Do South African Former Detainees Experience Post-Traumatic Stress? Circumventing the Demand Characteristics of Psychological Assessment

Most research on persons subjected to physical or psychological torture for political reasons has framed this experience as traumatic, with the sequelae approximating the diagnostic criteria of post-traumatic stress disorder (PTSD). Yet, critiques of the trauma model have called attention to the fact that PTSD represents a Western conceptualization of the concerns of persons who have survived stressful experiences. In order to determine whether symptoms of traumatization are salient psychiatric phenomena for South African former detainees, semi-structured qualitative interviews were conducted with 20 respondents who were detained and tortured for political reasons during the apartheid era. Interviews were transcribed and analysed for thematic content using a grounded theory approach. Results showed that although the main concerns expressed were unrelated to traumatization, participants also indicated that they experienced symptoms of post-traumatic stress. These data suggest that although too great a focus on traumatic responses may be misplaced, it remains important to consider the possibility that former detainees may exhibit symptoms of this nature. Consequently, critiques of the trauma discourse as a Western phenomenon need to be tempered with evidence of the lived reality of psychological sequelae experienced by this population.
TATA Box-Binding Protein–Associated Factor 12 Is Important for RAS-Induced Transformation Properties of Colorectal Cancer Cells

Activating mutations in the RAS proto-oncogene result in constant stimulation of its downstream pathways, further leading to tumorigenesis. Transcription factor IID (TFIID) can be regulated by cellular signals to specifically alter transcription of particular subsets of genes. To investigate potential links between the regulation of TFIID function and the RAS-induced carcinogenesis, we monitored the expression of the TATA box-binding protein and its associated factors (TAF) in human colon carcinoma cells. We primarily identified TAF12 levels as being up-regulated in cell lines bearing natural RAS mutations or stably overexpressing a mutated RAS isoform via a mitogen-activated protein kinase/extracellular signal-regulated kinase kinase–dependent pathway. We further showed by electrophoretic mobility shift assays and chromatin immunoprecipitation that the ETS1 protein was interacting with an ETS-binding site on the TAF12 promoter and was regulating TAF12 expression. The binding was enhanced in extracts from oncogenic RAS-transformed cells, pointing to a role in the RAS-mediated regulation of TAF12 expression. Reduction of TAF12 levels by small interfering RNA treatment induced a destabilization of the TFIID complex, enhanced E-cadherin mRNA and protein levels, and reduced migration and adhesion properties of RAS-transformed cells with epithelial to mesenchymal transition. Overall, our study indicates the importance of TAF12 in the process of RAS-induced transformation properties of human colon cells and epithelial to mesenchymal transition, most notably those related to increased motility, by regulating specifically expression of genes such as E-cadherin. (Mol Cancer Res 2008;6(6):1071–83)
Reduced expression of human mismatch repair genes in adult T‐cell leukemia

In this study, we investigated the expression of six human DNA mismatch repair (MMR) genes, human MutS homologues 2 (hMSH2), 3 (hMSH3), and 6 (hMSH6), human MutL homologue 1 (hMLH1), human post‐meiotic segregations 1 (hPMS1) and 2 (hPMS2), in primary leukemic cells obtained from 11 patients with acute‐type adult T‐cell leukemia (ATL) by using reverse transcription–polymerase chain reaction (RT‐PCR). In contrast to normal peripheral lymphocytes, all primary ATL samples had reduced or loss of expression of two or more MMR genes, and the expression of several MMR genes was simultaneously suppressed in each ATL patient. Abnormal expression of hMSH2, hMSH3, hMSH6, hMLH1, and hPMS1 was observed more frequently than that of hPMS2. In particular, expression of hMSH2 and hPMS1 was reduced in all cases. Western blot analysis further showed reduced expression of both hMSH2 and hPMS1 proteins in all five cases examined. In three out of the 5 cases, both of the two proteins were undetectable. Interestingly, methylation‐specific PCR indicated methylation of hPMS1 promoter in all of four ATL cases examined. hPMS1 expression, but not hMSH2 expression, was restored by treatment with a DNA demethylation agent, 5‐aza‐2′‐deoxycytidine, suggesting that methylation plays a crucial role in inhibition of the hPMS1 gene expression in ATL. Our results demonstrate that defect of both human MutS and human MutL systems in primary ATL cells. Am. J. Hematol. 78:100–107, 2005. © 2005 Wiley‐Liss, Inc.
The occurrence of immunological disturbances in patients with recurrent miscarriage (RM) of unknown etiology.

OBJECTIVE The 155 patients suffering from primary RM who took part in this study were qualified after excluding known causes of abortions. METHODS The presence of the following immunological factors was examined in serum samples: autoantibodies such as anti-cardiolipin (ACA) IgG and IgM, lupus-anticoagulant (LA), anti-thyroid (ATA): anti-thyroglobulin (anti-TG) and anti-thyroid peroxydase (anti-TPO), anti-nuclear (ANA), anti-placental (APA) antibodies and alloimmunological disturbances following HLA-class I antibody test (LCT-lymphocytotoxic test), lack of blocking proliferative activity in mixed lymphocyte reaction test (MLR), anti-sperm (ASA) antibodies, levels of extracellular interferon γ (IFN γ) and tumour necrosis α (TNFα) produced by peripheral blood lymphocytes. RESULTS Immunological disturbances were found in 69.1% of the patients suffering from primary RM of unknown etiology. The number of RM correlated with the frequency of immunological disturbance. Among the samples from patients who underwent ≥5 RM, positive levels of TNFα were the most frequently observed risk factor (up to 27%) (p=0.05). Although the incidence of immunological factors was comparable between patients with early and late pregnancy losses, elevated ATA levels were frequently seen among late miscarriage (95% CI=36.0, p≤0.01). CONCLUSION The heterogeneity of immunological risk factors shown in this study indicates the usefulness of detecting alloimmune factors as well as autoantibodies in patients with RM of unknown etiology. This may be helpful to analyse the therapeutical effectivity of various treatment in a better characterized group of patients and to explain unsuccessful results of treatment in patients with RM of unknown etiology.
Urochloa ruziziensis responses to sources and doses of urea

The use of products that promote reduction of nitrogen (N) losses from the urea fertilizer can contribute to increasing its use efficiency in forage grasses. This study aimed to evaluate the effects of N sources and doses on the growth of Urochloa ruziziensis. The experiment was carried out in the growing season of 2007/2008 in Santo Antonio de Goias-GO, in a Brazilian Oxisol. A completely randomized block was used, with four replicates in a factorial scheme, corresponding to two N sources (conventional urea and urea with urease inhibitor) and five N doses (0, 50, 100, 200 and 300 kg ha-1), divided into equal applications in five periods (Nov 14 to Dec 13, Dec 14 to Jan 12, Jan 13 to Feb 11 - rainy season, Mar 24 to Apr 22 and Jul 10 to Aug 08 - dry season). The effects of the treatments were evaluated for: shoot dry matter, tiller density, total N content in the leaves and relative chlorophyll content. N fertilizer sources did not affect the evaluated variables; however, N fertilization allowed linear increases in all variables with higher values during the rainy period. The relative chlorophyll content in U. ruziziensis had positive correlation with its dry matter productivity.
The presence of rRNA sequences in polyadenylated RNA and its potential functions

Accumulating evidence has shown that various lengths of ribosomal RNA (rRNA) sequences are widely present in polyadenylated RNA. This review article will discuss these polyadenylated rRNAcontaining transcripts (PART). PART are highly abundant and widely expressed in various tissues. It appears that there may be two types of PART. One type, type I, contains the rRNA segments (from ∼10 nucleotides up to several hundred nucleotides) located within the transcripts. It has been demonstrated that short rRNA sequences within type I PART may function as cis‐regulatory elements that regulate translational efficiency. The other type, type II, contains large portions or almost entire sequences of rRNA with a cap at the 5' end and poly(A) at 3' end. Recent work has shown that some type II PART have functional significance for some neurodegenerative disease processes and may play an important role in the pathogenesis of diseases. Further investigation in this area is critical to understanding the basic biology of PART and the potential role of PART in diseases.
Monetary Sanctions: Toward a Socio-Cultural Theory of

Recent research suggests that the use of monetary sanctions as a supplementary penalty in state and federal criminal courts is expanding, and that their imposition creates substantial and deleterious legal debt. Little is known, however, about the factors that influence the dis cretionary imposition of these penalties. This study offers a comprehensive account of the role socio-cultural factors, especially race and ethnicity, have in this institutional sanctioning process. We rely on multilevel statistical analysis of the imposition of monetary sanctions in Washington State courts to test our theory. The theoretical framework emphasizes the need to treat race and ethnicity as complex cultural categories, the meaning and institutional effects of which may vary across time and space. Findings indicate that racialized crime scripts, such as the association of Latinos with drugs, affect defendants whose wrong-doing is stereo type congruent. Moreover, all individuals accused of committing racially and ethnically stig matized offenses in racialized contexts may experience the courtesy stigma that flows from racialization. We find that race and ethnicity are not just individual attributes but cultural categories that shape the distribution of stigma and the institutional consequences that flow from it.
Effects of stride frequency and foot position at landing on braking force, hip torque, impact peak force and the metabolic cost of running in humans

ABSTRACT Endurance runners are often advised to use 90 strides min−1, but how optimal is this stride frequency and why? Endurance runners are also often advised to maintain short strides and avoid landing with the feet too far in front of their hips or knees (colloquially termed ‘overstriding’), but how do different kinematic strategies for varying stride length at the same stride frequency affect economy and impact peaks? Linear mixed models were used to analyze repeated measures of stride frequency, the anteroposterior position of the foot at landing, V̇O2, lower extremity kinematics and vertical ground reaction forces in 14 runners who varied substantially in height and body mass and who were asked to run at 75, 80, 85, 90 and 95 strides min−1 at 3.0 m s−1. For every increase of 5 strides min−1, maximum hip flexor moments in the sagittal plane increased by 5.8% (P<0.0001), and the position of the foot at landing relative to the hip decreased by 5.9% (P=0.003). Higher magnitudes of posteriorly directed braking forces were associated with increases in foot landing position relative to the hip (P=0.0005) but not the knee (P=0.54); increases in foot landing position relative to the knee were associated with higher magnitudes (P<0.0001) and rates of loading (P=0.07) of the vertical ground reaction force impact peak. Finally, the mean metabolically optimal stride frequency was 84.8±3.6 strides min−1, with 50.4% of the variance explained by the trade-off between minimizing braking forces versus maximum hip flexor moments during swing. The results suggest that runners may benefit from a stride frequency of approximately 85 strides min−1 and by landing at the end of swing phase with a relatively vertical tibia. Summary: Variation in stride frequency and foot position at landing affects the cost of running and the generation of impact peaks in human runners.
Glottic configuration in patients with exercise‐induced stridor: A new paradigm

Paradoxical vocal fold motion and exercise‐induced paradoxical vocal fold motion (EIPVFM) are two related conditions that do not have definitive diagnostic criteria. Much of the EIPVFM literature describes patients with characteristic physiologic findings of severe upper airway obstruction or obvious airflow limitation in the clinical context of exertional dyspnea with audible stridor. The objective of this study was to highlight a group of patients who demonstrate important clinical findings of EIPVFM (exertional dyspnea with audible stridor) without simultaneously definitive physiologic findings (mild glottic adduction and normal flow volume loops).
Enhanced Photoresponsivity From Hybrid-ZnO Nanowires With White LED 400–700-nm Illumination

This paper highlights the photoresponsivity property of a hybrid-ZnO nanowire (ZnO NW) photodetector to a white LED source with a wavelength range of 400–700 nm. The use of methanol via the vapor phase transport method was utilized to achieve the incorporation of carbon and oxygen particles with Zn to form hybrid-ZnO NWs. Field emission scanning electron microscope, X-ray diffraction, and Raman scattering techniques were used in the identification of morphology, polycrystalline structure, and <inline-formula> <tex-math notation="LaTeX">${D}$ </tex-math></inline-formula>-, <inline-formula> <tex-math notation="LaTeX">${G}$ </tex-math></inline-formula>-, and 2-D bands, respectively. Positive photoresponsivity and negative photoresponsivity of the hybrid-ZnO NWs were studied with the LED distances 1–4 cm from the hybrid-ZnO NWs for varied bias voltage from 1 to 4 V. A reproducible photoresponsivity with response times ranging from 182 to <inline-formula> <tex-math notation="LaTeX">$345~\mu \text{s}$ </tex-math></inline-formula> was measured using an oscilloscope. The proposed technique demonstrates the great potential possessed by hybrid-ZnO NWs in optoelectronic applications in the near future.
Ammonium Production by Dissimilatory Nitrate Reducers Isolated from Baltic Sea Water, as Indicated by 15N Study

Bacteria able to perform dissimilatory nitrate reduction to ammonium were isolated from low-oxygen masses in the Baltic Sea. In liquid media enriched with 15NO3− and incubated anaerobically, the NH4+-producing isolates transformed 25 to 72% of the 15NO3− to 15NH4+.
Coupled free-carrier and exciton relaxation in optically excited semiconductors.

The energy relaxation of coupled free-carrier and exciton populations in semiconductors after low-density ultrafast optical excitation is studied through a kinetic approach. The set of semiclassical Boltzmann equations, usually written for electron and hole populations only, is complemented by an additional equation for the exciton distribution. The equations are coupled by reaction terms describing phonon-mediated exciton binding and dissociation. All the other relevant scattering mechanisms, such as carrier-carrier, carrier-phonon, and exciton-phonon interactions, are also included. The resulting system of rate equations in reciprocal space is solved by an extended ensemble Monte Carlo method. As a first application, we show results for the dynamics of bulk GaAs in the range from 1 to ∼200 ps after photoexcitation. The build-up of an exciton population and its sensitivity to the excitation conditions are discussed in detail. As a consequence of the pronounced energy dependence of the LO-phonon-assisted transition probabilities between free-pair states and excitons, it is found that the efficiency of the exciton-formation process and the temporal evolution of the resulting population are sensitive to the excitation energy. We discuss the effects on luminescence experiments.
Ceruminous Adenomas: A Clinicopathologic Study of 41 Cases With a Review of the Literature

Background:Ceruminous gland neoplasms are rare neoplasms. To date, a large clinicopathologic study of benign ceruminous gland neoplasms has not been reported. Design:Forty-one cases of ceruminous gland adenomas diagnosed between 1970 and 2000 were retrieved from the files of the Armed Forces Institute of Pathology. Histologic features were reviewed, immunohistochemical analysis was performed (n = 21), and patient follow-up was obtained (n = 40). Results:The patients included 22 men and 19 women, 24 to 85 years of age (mean, 54.2 years). Patients presented clinically with a painless mass of the outer half of the external auditory canal (n = 33) or with hearing changes (n = 11). Symptoms were present for an average of 16.3 months. The polypoid masses affected the external auditory canal only and ranged in size from 0.4 to 2 cm in greatest dimension (mean, 1.1 cm). Histologically, the tumors demonstrated glands and small cysts lined by a tubuloglandular proliferation of inner ceruminous cells (cerumen-secreting epithelium with decapitation secretion) subtended by a spindled to cuboidal myoepithelial layer. A hyalinized stroma created an infiltrative pattern of growth; surface involvement (n = 8) was seen. Tumors were divided into ceruminous adenoma (n = 36), ceruminous pleomorphic adenoma (n = 4), and syringocystadenoma papilliferum (n = 1) types. The luminal cells were strongly and diffusely immunoreactive with CK7, while the basal cells were highlighted with CK5/6, S-100 protein, and p63. CD117 highlighted the luminal cells preferentially. The proliferation markers revealed a low index. Adenocarcinoma and middle ear adenoma are the principal differential consideration. Surgical excision was used in all patients. Four patients developed a recurrence due to incomplete excision. All patients were without evidence of disease at the last follow-up: alive (n = 28, mean 16.3 years) or dead (n = 12, mean 11.8 years). Conclusion:Ceruminous gland adenomas are the most common external auditory canal tumors. They demonstrate a dual cell population of basal myoepithelial-type cells and luminal ceruminous (ceruminal) cells. Cerumen pigment, CK7, and p63 can help to distinguish this tumor from other neoplasms that occur in the region. Complete surgical excision results in an excellent long-term clinical outcome.