Miracle-dz/UniFAR-FTUs huggingface dataset:
The Typically Mitochondrial DNA-encoded ATP6 Subunit of the F1F0-ATPase Is Encoded by a Nuclear Gene in Chlamydomonas reinhardtii *

The atp6 gene, encoding the ATP6 subunit of F1F0-ATP synthase, has thus far been found only as an mtDNA-encoded gene. However, atp6is absent from mtDNAs of some species, including that ofChlamydomonas reinhardtii. Analysis of C. reinhardtii expressed sequence tags revealed three overlapping sequences that encoded a protein with similarity to ATP6 proteins. PCR and 5′- and 3′-RACE were used to obtain the complete cDNA and genomic sequences of C. reinhardtii atp6. Theatp6 gene exhibited characteristics of a nucleus-encoded gene: Southern hybridization signals consistent with nuclear localization, the presence of introns, and a codon usage and a polyadenylation signal typical of nuclear genes. The corresponding ATP6 protein was confirmed as a subunit of the mitochondrial F1F0-ATP synthase from C. reinhardtii by N-terminal sequencing. The predicted ATP6 polypeptide has a 107-amino acid cleavable mitochondrial targeting sequence. The mean hydrophobicity of the protein is decreased in those transmembrane regions that are predicted not to participate directly in proton translocation or in intersubunit contacts with the multimeric ring of c subunits. This is the first example of a mitochondrial protein with more than two transmembrane stretches, directly involved in proton translocation, that is nucleus-encoded.
Evaluations of Different Hypervariable Regions of Archaeal 16S rRNA Genes in Profiling of Methanogens by Archaea-Specific PCR and Denaturing Gradient Gel Electrophoresis

ABSTRACT Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.
Intraretinal analysis of the threshold dark-adapted ERG of cat retina.

1. The dark-adapted electroretinogram (ERG) obtained with 4-s flashes near threshold and at low intensities has three clear negative components: 1) a fast negative response at stimulus onset, 2) a slow negative response that increases in amplitude for about 2 s, and 3) a negative-going OFF response. The fast negative response was previously shown to originate from the scotopic threshold response (STR) arising in the proximal portion of neural retina. We investigated the intraretinal origins of the other two negative components and found that they also have origins in neural retina proximal to the photoreceptors. 2. In this study the ERG evoked in response to diffuse illumination of the dark-adapted cat retina was recorded between a chlorided silver wire in the vitreous and a plate behind the eye. Extracellular field potentials were recorded simultaneously with a microelectrode placed intraretinally at different retinal depths. In some cases light-dependent changes in extracellular K+ concentration ([K+]o) were recorded with the K+-selective barrel of a double-barreled microelectrode. 3. The three negative-going ERG potentials increased in amplitude from threshold up to approximately 6.0 log q.deg-2.s-1. The potential during illumination then became nearly flat, and the negative OFF response was exaggerated. At higher intensities, positive-going PII (DC-component and b-wave) and the c-wave emerged, whereas the a-wave (negative-going) was usually below threshold. 4. The slow negative ERG response was generated in neural retina, rather than by the retinal pigment epithelium. The response was positive-going in the transretinal recordings obtained in subretinal space. It was not, however, related to two positive-going responses from distal retina previously described as contributing negative components to the ERG: the neural retina component of the c-wave, termed slow PIII, and the rod-receptor potential. The slow negative response had a slower time course and lower threshold than slow PIII, and, more importantly, it was present in the absence of the [K+]o decrease in subretinal space that causes slow PIII. Furthermore, APB (1.2 mM vitreal concentration) blocked the entire negative-going ERG, whereas at higher intensities it blocked PII but not the c-wave in the ERG or slow PIII in transretinal recordings. These results indicate that the negative-going ERG components near threshold and at low intensities all originated proximal to the photoreceptors. (ABSTRACT TRUNCATED AT 400 WORDS)
From protein interaction profile to functional assignment: The human protein Ki-1/57 is associated with pre-mRNA splicing events

The mapping of protein-protein interactions of a determined organism is considered fundamental to assign protein function in the post-genomic era. As part of this effort, screenings for pairwise interactions by yeast two-hybrid system have been used popularly to reveal protein interaction networks in different biological systems. Through the identification of protein interaction partners we have successfully obtained interesting functional clues for Ki-1/57, a human protein with no previous functional annotation, in the context of RNA metabolism. We briefly discuss here the way we approached protein-protein interaction data to conduct and interpret further molecular biological and cellular studies as well as structural analyses on this protein. Our data suggest that Ki-1/57 belongs to the family of intrinsically unstructured proteins and that the structural flexibility may be crucial for its capacity to interact with many different proteins. A large fraction of these proteins are involved in pre-mRNA splicing control. Finally, Ki-1/57 is localized to several subnuclear domains, all of which have been described to splicing and other RNA processing events.
Phagocytosis and intracellular killing of pathogenic yeasts by human monocytes and neutrophils

The kinetics of phagocytosis and killing of four fungal forms with varying virulence by two types of phagocytic cells was examined. Human monocytes ingested Saccharomyces cerevisiae, Candida tropicalis, and the blastospores of Candida albicans more rapidly than did human neutrophils. There was no difference in the rate of phagocytosis of C. albicans pseudohyphae by these two cell types. Intracellular killing of each of the four fungal forms was consistently and significantly more rapid by monocytes than by neutrophils. Neutrophils were unable to destroy ingested C. albicans pseudohyphae. These experiments suggest that the monocyte plays an important role in host defenses against fungal diseases and that the relative virulence of the pathogenic yeasts in human disease may be related to the ability of these organisms to survival after being ingested by circulating phagocytes.
Quantitative aspects of the state‐dependent co‐variation of cat lateral geniculate and perigeniculate visual activity

The quantitative relationship between EEG-related changes in the visual activity of perigeniculate (PGN) and lateral geniculate (LGN) neurons with overlapping receptive (r)elds was analyzed in the anesthetized and paralyzed cat. While transient response peaks were independent of the EEG state, we found opposite changes in spontaneous activity and tonic visual responses, with PGN cells increasing and LGN cells decreasing their spontaneous/tonic activity with increasing EEG delta activity in most cases. The tonic (r)ring rates of PGN and LGN cell pairs were clearly correlated with a slope of about −0.5. Thus, LGN (r)ring was low when PGN activity was high and vice versa. With a change from low to high EEG delta activity the difference between the tonic responses of PGN and LGN cells increased on average by 50 spikes/s, both for the whole population and at the single cell level, indicating that state-dependent changes in retino-geniculate transmission are regulated by a distinct ratio of PGN-LGN activity.
A functional toll-like receptor 8 variant is associated with HIV disease restriction.

BACKGROUND Toll-like receptors (TLRs) play an important role in the innate immune response to pathogens. TLR8 has been found to recognize RNA derived from various viruses, including human immunodeficiency virus (HIV). Presently, very little is known about the influence of TLR8 genetic variation on susceptibility to and progression of HIV disease. METHODS AND RESULTS We genotyped a population of 782 HIV-positive adults and 550 healthy control subjects for 3 nonsynonymous TLR8 single-nucleotide polymorphisms. We found that the presence of the most frequent TLR8 polymorphism, TLR8 A1G (rs3764880), confers a significantly protective effect regarding progression of the disease. In overexpression assays, we demonstrated that this receptor variant displays impaired NF-kappaB activation in vitro. Furthermore, we analyzed different cell types obtained from individuals differing in their TLR8 genotype and assessed their response to TLR8 ligands in vitro. The presence of the mutated receptor variant was associated with modulation of cytokine secretion profiles and lipid mediator synthesis patterns in monocytes and neutrophils. CONCLUSIONS This first report of a functional TLR8 variant associated with a different clinical course of an RNA viral disease may have implications for the individual risk assessment of patients infected with HIV and other RNA viruses as well as for future HIV vaccine development.
PARAMETRIC CODING OF SPATIAL AUDIO

A wide range of techniques for coding a single speech or audio signal channel have been developed over the last few decades. In addition to pure redundancy reduction, sophisticated source and receiver models have been considered for reducing the bitrate. Only a few techniques address joint-coding of the channels of stereo1 and multi-channel audio signals. Stereo and multi-channel audio signals evoke an auditory spatial image in a listener. Thus the receiver model may consider properties of spatial hearing of the auditory system for reducing the bitrate. This has been done in previous techniques by considering the importance of interaural level difference cues at high frequencies and by considering the binaural masking level difference for computing the masked threshold for multiple audio channels. The coding scheme proposed in this thesis aims at being more systematic and parameterized. A stereo or multi-channel audio signal is represented as a single downmixed audio channel plus side information. The side information contains the inter-channel cues inherent in the original audio signal that are relevant for the perception of the properties of the auditory spatial image. At the decoder the stereo or multi-channel audio signal is reconstructed such that its inter-channel cues approximate the corresponding cues of the original audio signal. This enables coding of stereo or multi-channel audio signals at a bitrate nearly as low as a mono audio coding bitrate because the side information contains about two orders of magnitude less information than the original audio channel waveforms. This corresponds to a significant bitrate reduction compared to conventional state-of-the-art coders. Several subjective tests were conducted, indicating that good audio quality can be achieved by the proposed scheme. A number of variations of the coding scheme are proposed. These include different combinations of conventional multi-channel audio coders and the proposed coding scheme, and a scheme which provides flexibility at the decoder to manipulate the auditory spatial image. A model for source localization in the presence of concurrent sound (other sources and reflections) is proposed. The results from a number of previous psychophysical studies are predicted successfully by the model. The model is also applied for comparing audio signals to corresponding signals coded with the proposed scheme. 1In this thesis, the term "stereo audio signal" always refers to two-channel stereo audio signals.
The Behavior of Ethicists

Arguably, one of the aims of studying ethics is moral self‐improvement. In ancient philosophy, moral self‐improvement is often treated as the foremost aim for the student of ethics – for example, in Aristotle (fourth‐century BCE/1962), Confucius (fifth‐century BCE/2003), and Epictetus ( second‐century CE/2008). Twentieth‐ and twenty‐first‐century philosophers might overall tend to aim their ethical reflections more toward theoretical discovery than toward self‐improvement, but moral self‐improvement plausibly remains among the goals of a significant portion of professional ethicists to the extent they use their philosophical training in ethics to help them reflect on, for example, to what extent they have a duty to donate to charity or whether it is morally permissible to eat meat, with the thought of acting upon their conclusions. Two related questions thus invite empirical treatment: Is philosophical moral reflection of the sort practiced by professional ethicists in fact morally improving? And how do professional ethicists’ explicitly espoused moral principles relate to their practical moral behavior? Individual ethicists’ lives are sometimes examined with these questions in mind, especially the life of Martin Heidegger, notorious for his endorsement of Nazism (e.g., Sluga 1993; Young 1997; Faye 2005/2009); and general claims about the behavior of ethicists are sometimes made based on personal experience or broad plausibility considerations (e.g., Posner 1999; Knobe and Leiter 2007; Moeller 2009). However, until recently, systematic, quantitative research on these issues has been entirely lacking. To date, all published quantitative studies of the issue have been led by Eric Schwitzgebel and Joshua Rust, the two authors of this chapter, mostly in collaboration with each other. Our general finding is this: On average, professional ethicists’ behavior is indistinguishable from the behavior of comparison groups of professors in other fields. Also, in one multivariable study, we find ethicists neither more nor less likely than other professors to act in accord with their expressed moral attitudes. The Behavior of Ethicists
The Influence of Family and Social Factors on the Course of Psychiatric Illness

Summary This study is a replication and extension of past work carried out by Brown, Birley and Wing (1972) concerning the influence of family life on the course of schizophrenia. In the original research the index of emotion expressed by a key relative about the patient at the time of key admission proved to be the best single predictor of symptomatic relapse in the nine months after discharge from hospital. In the present study this main finding of Brown et al has been replicated for two clinically different groups of psychiatric patients. The expressed emotion of the relative again seems to be associated with relapse independently of all other social and clinical factors investigated. In addition, important additive effects between various social influences and pharmacological treatments have been revealed which make it possible to predict relapse patterns in schizophrenia with considerable precision. The patterns of these relationships with relapse are different for the two clinical groups studied, patients with schizophrenic psychosis and with depressive neurosis.
An Introduction of a Financial Model for the Australian Higher Education

This study examines the global trend in shifting university costs from national governments to individual students and families, with a specific focus on the existing cost-sharing model in Australian higher education. The Australian system is worthy of consideration by other nations as a possible mechanism for enhancing access to higher education for individuals who might otherwise not possess the opportunity to participate.
Angular and Rotational Profile of the Lower Limb in 2,630 Chinese Children

Angular and rotational profile of the lower limbs of 2,630 normal Chinese children from newborn to age 12 years were compiled using tibiofemoral angle, intercondylar, intermalleolar distance, medial and lateral rotation of the hip, and thigh-foot angle. Children with clinical tibiofemoral angles, intercondylar or intermalleolar distances tended to be bowlegged at birth, maximally knock-kneed at age 3 and to have normal lower limbs by age 8. Medial hip rotation increased steadily from birth to a maximum of 56° at age 9, and lateral hip rotation decreased from birth to a minimum of 30° at age 9. Significant differences between Chinese children and children of other races were highlighted.
Natural Compounds as Anticancer Agents Targeting DNA Topoisomerases

DNA topoisomerases are important cellular enzymes found in almost all types of living cells (eukaryotic and prokaryotic). These enzymes are essential for various DNA metabolic processes e.g. replication, transcription, recombination, chromosomal decatenation etc. These enzymes are important molecular drug targets and inhibitors of these enzymes are widely used as effective anticancer and antibacterial drugs. However, topoisomerase inhibitors have some therapeutic limitations and they exert serious side effects during cancer chemotherapy. Thus, development of novel anticancer topoisomerase inhibitors is necessary for improving cancer chemotherapy. Nature serves as a repertoire of structurally and chemically diverse molecules and in the recent years many DNA topoisomerase inhibitors have been identified from natural sources. The present review discusses anticancer properties and therapeutic importance of eighteen recently identified natural topoisomerase inhibitors (from the year 2009 to 2015). Structural characteristics of these novel inhibitors provide backbones for designing and developing new anticancer drugs.
Two‐temperature stage biphasic CO2–H2O pretreatment of lignocellulosic biomass at high solid loadings

Most biomass pretreatment processes for monosaccharide production are run at low‐solid concentration (<10 wt%) and use significant amounts of chemical catalysts. Biphasic CO2–H2O mixtures could provide a more sustainable pretreatment medium while using high‐solid contents. Using a stirred reactor for high solids (40 wt%, biomass water mixture) biphasic CO2–H2O pretreatment of lignocellulosic biomass allowed us to explore the effects of particle size and mixing on mixed hardwood and switchgrass pretreatment. Subsequently, a two‐temperature stage pretreatment was introduced. After optimization, a short high‐temperature stage at 210°C (16 min for hardwood and 1 min for switchgrass) was followed by a long low‐temperature stage at 160°C for 60 min. Glucan to glucose conversion yields of 83% for hardwood and 80% for switchgrass were obtained. Total molar sugar yields of 65% and 55% were obtained for wood and switchgrass, respectively, which consisted of a 10% points improvement over those obtained during our previous study despite a 10‐fold increase in particle size. These yields are similar to those obtained with other major pretreatment technologies for wood and within 10% of major technologies for switchgrass despite the absence of chemical catalysts, the use of large particles (0.95 cm) and high solid contents (40 wt%). Biotechnol. Bioeng. 2012; 109:1499–1507. © 2011 Wiley Periodicals, Inc.
Effect of human somatotropin-releasing factor and photoperiods on carcass parameters and mammary gland development of dairy heifers.

Forty-eight heifers (3 mo old) were subjected for 35 wk to twice daily s.c. injections of saline or human somatotropin-releasing factor (5 microgram.kg-1 BW) and photoperiod of 8 h (short day) or 16 h (long day) of light daily according to a 2 X 2 factorial design. There was no treatment effect on slaughter weight, withers height, and carcass length. Somatotropin-releasing factor increased thymus weight, metacarpal length, and protein content of the carcass but decreased carcass fat content. Long day photoperiod increased chest girth, pituitary weight, and carcass yield. Effects of somatotropin-releasing factor and photoperiod were not additive on volume of mammary parenchymal tissue; there was also a treatment interaction on liver and lung weights. However, extraparenchymal mammary tissue was decreased by human somatotropin-releasing factor and short day photoperiod. In conclusion, use of somatotropin-releasing factor and photoperiod treatments affected carcass parameters and composition and mammary growth.
A Mutant of Paracoccus denitrificans with Disrupted Genes Coding for Cytochrome c550 and Pseudoazurin Establishes These Two Proteins as the In Vivo Electron Donors to Cytochrome cd1 Nitrite Reductase

ABSTRACT In Paracoccus denitrificans, electrons pass from the membrane-bound cytochrome bc1 complex to the periplasmic nitrite reductase, cytochrome cd1. The periplasmic protein cytochrome c550 has often been implicated in this electron transfer, but its absence, as a consequence of mutation, has previously been shown to result in almost no attenuation in the ability of the nitrite reductase to function in intact cells. Here, the hypothesis that cytochrome c550 and pseudoazurin are alternative electron carriers from the cytochrome bc1 complex to the nitrite reductase was tested by construction of mutants of P. denitrificans that are deficient in either pseudoazurin or both pseudoazurin and cytochrome c550. The latter organism, but not the former (which is almost indistinguishable in this respect from the wild type), grows poorly under anaerobic conditions with nitrate as an added electron acceptor and accumulates nitrite in the medium. Growth under aerobic conditions with either succinate or methanol as the carbon source is not significantly affected in mutants lacking either pseudoazurin or cytochrome c550 or both these proteins. We concluded that pseudoazurin and cytochrome c550 are the alternative electron mediator proteins between the cytochrome bc1 complex and the cytochrome cd1-type nitrite reductase. We also concluded that expression of pseudoazurin is mainly controlled by the transcriptional activator FnrP.
BIOTYPES OF CAPSULATED AND NON‐CAPSULATED HAEMOPHILUS INFLUENZAE. Correlation between Biotypes andβ‐Lactamase Production

396 Haemophilus influenzae strains were biotyped according to Kilian. 393 of the strains were assigned to biotypes I to V, while 3 strains remained unclassified. Eighty‐nine per cent of the capsulated strains produced both urease and ornithine decarboxylase, biotypes I or IV, while 95 per cent of the non‐capsulated strains produced only one of the enzymes, biotypes II, III, or V. Of consecutive strains from the upper respiratory tract, the incidence ofβ‐lactamase‐positive strains was higher among capsulated than among non‐capsulated strains (p< 0.025). None of 133 non‐capsulatedβ‐lactamase‐positive strains produced both urease and ornithine decarboxylase, in contrast to 15 out of 147 non‐capsulatedβ‐lactamase‐negative strains (p< 0.001). The type e strains were all of biotype IV and 3 of 7 consecutive strains wereβ‐lactamase‐positive.