Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of backrest elevation in critical care: a pilot study.

BACKGROUND Use of lower backrest positions occurs frequently and is a factor in the development of ventilator-associated pneumonia. OBJECTIVES To determine the usual bed elevation and backrest position in a medical intensive care unit and their relationship to hemodynamic status and enteral feeding. METHODS Data were collected in a 12-bed medical respiratory intensive care unit for 2 months. A protractor was used to measure the elevation of the head of the bed. Hemodynamic status was defined by systolic, diastolic, and mean arterial blood pressure measurements retrieved from each patient's flow sheet. RESULTS The sample included 347 measurements of 52 patients. Mean backrest elevation was 22.9 degrees, and 86% of patients were supine. Backrest position differed significantly (P = .005) among nursing shifts (days, evenings, nights) but not for systolic (r = -0.04, P = .49), diastolic (r = 0.01, P = .83), or mean arterial blood pressure (r = -0.01, P = .84). Backrest elevation did not differ significantly between patients who were receiving enteral feedings and patients who were not (P = .23) or between patients receiving intermittent versus continuous nutrition (P = .22). CONCLUSIONS Use of higher levels of backrest elevation (> or = 30 degrees) is minimal and is not related to use of enteral feeding or to hemodynamic status. The rationale for using lower backrest positions for critically ill patients may be based on convenience, the patient's comfort, or usual patterns in the unit. However, the dangers of supine positioning and its relationship to aspiration and ventilator-associated pneumonia should not be minimized.
Endocytosis: A Positive or a Negative Influence on Wnt Signalling?

Endocytosis, with subsequent targeting to lysosomes for degradation, is traditionally seen as a way for cells to terminate signalling. However, in a few instances, endocytosis has been demonstrated to contribute positively to signalling. Here we review recent work on the role of endocytosis in Wnt signalling. Biochemical evidence suggests that the branch of Wnt signalling that controls planar cell polarity (PCP) does require endocytosis, although how endocytosis of Frizzled receptors is translated into PCP in vivo remains unknown. With respect to the main signalling branch (called the canonical or β‐catenin pathway), the literature is divided as to whether endocytosis is required. Results of in vivo experiments are inconclusive because of the toxic side‐effects of blocking endocytosis. Some results with cultured cells suggest the need for endocytosis in canonical signalling; however, it remains unclear whether the ligand–receptor complex must enter the cell by clathrin‐mediated or caveolae‐mediated endocytosis in order to signal. Means of specifically altering Wnt trafficking as well as of tracking the internalization route in different cell types are needed.
Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN]

Conservation, neofunctionalization, and specialization are main evolutionary trajectories for Arabidopsis young duplicate genes, and their relative roles change dynamically over evolutionary time. Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.
Parkinson's disease in Ireland: Clinical presentation and genetic heterogeneity in patients with parkin mutations

Early‐onset autosomal recessive parkinsonism is associated with parkin gene mutations. Different parkin mutations occur in many ethnic backgrounds; however, the phenotype may vary. We studied 102 young‐onset (age at onset <60 years) Parkinson's disease (PD) patients. From 102 patients, 40 with early‐onset PD (<45 years at symptomatic onset) were selected for clinical assessment and parkin gene molecular analysis for duplications/deletions and point mutations. We identified parkin mutations in 7 of 40 early‐onset patients; including novel compound heterozygotes and potential splice site changes. The mean age at onset in the 7 parkin mutation‐positive patients was 33 ± 9 years (age range, 18–42 years), marginally lower than that of the 33 parkin‐negative early‐onset patients, 38 ± 7 years (age range, 17–45 years). A family history of PD was present in 4 of 7 patients with parkin mutations, compared with 6 of 33 early‐onset parkin‐negative patients. Overall, parkin mutations were found in 4 of 10 patients with a positive family history and 3 of 30 patients without a family history of PD. Patients with parkin mutations had more dystonia, dyskinesia, and sleep benefit compared with parkin‐negative patients. We subsequently identified a single point mutation among the 62 young‐onset (age at onset 45 to <60 years). Mutations in the parkin gene may account for ∼17% of early‐onset (age at onset <45 years) parkinsonism in Ireland, in agreement with previous European studies. © 2003 Movement Disorder Society
Radiation-Induced Necrosis of the Temporal Bone: Diagnosis and Management

Objective To document our experience with osteoradionecrosis (ORN) of the temporal bone. Study Design Retrospective case review. Setting Tertiary care medical center. Patients Patients who developed exposed necrotic bone of the external auditory canal after radiation therapy to the head and neck. Interventions Temporal bone ORN was managed conservatively in all patients with a combination of systemic antibiotics, antibiotic ear drops, and in-office debridement. Three patients required surgery, two of which were for a cholesteatoma. Main Outcome Measure The need for surgical intervention in the management of ORN. Results Twenty-three patients with ORN of the temporal bone comprise the study group. The average age of patients at the time of diagnosis was 58 years (range, 34–75 yr). The parotid gland was the most common primary tumor site (n = 10). The mean lag time from completion of radiotherapy to diagnosis of ORN was 11 years (range, 2–48 yr). The most common presenting symptom was hearing loss (n = 18), followed by tinnitus (n = 13) and otorrhea (n = 13). All 23 patients were managed conservatively with antibiotic therapy and in-office debridement of necrotic bone. None of the patients required temporal bone resection and/or free-flap reconstruction. Conclusion ORN of the temporal bone is a rare adverse event that can occur after radiotherapy for a variety of neoplasms of the head, neck, and central nervous system. Conservative management, which includes directed antibiotic therapy and regular in-office debridement of necrotic bone, can adequately control the disease process and symptomatology, thus avoiding more invasive surgical interventions.
Responses of the Steroid Circadian System to Alcohol in Humans: Importance of the Time and Duration of Intake

Reports provide conflicting data about the effects of alcohol consumption on the hormonal system. Any study of these effects must control for a number of variables, including sex, alcohol status (alcoholic addiction vs. non-addiction), medical status (malnutrition, liver disease), and conditions of alcohol exposure, including an acute or continuous pattern of intake. The latter appears to be an especially critical factor in interpreting these effects. The authors therefore conducted a trial with a circadian design in which alcohol was administered repeatedly and regularly over a 26 h period for a total dose of 256 g. Because this protocol involves continuous alcohol administration, it is similar to administration among alcoholics and thus sheds new light on alcohol's effect on hormone secretion. Using healthy volunteers rather than alcoholics, however, prevents any confounding due to liver disorders and nutritional deficiencies, and thus makes it possible to focus on the direct role of alcohol in hormonal modifications. In these conditions, the continuous administration of alcohol did not affect cortisol secretion, but serum testosterone levels were significantly higher at all time points during the alcohol session than at the corresponding time points during the control session. These data are not consistent with previously reported findings for the relation between alcohol and both cortisol and testosterone, because in the current experiment the action of ethanol on steroid secretion should involve the circadian clock more than the hormonal system itself.
Cancer screening behaviors and attitudes of women in southeastern Minnesota.

OBJECTIVES To determine the rates at which women received screening Papanicolaou tests, clinical breast examinations, and mammography and to determine the extent to which these women might be expected to respond to screening recommendations from their physicians. DESIGN Random-digit-dial telephone interviews conducted in January 1993. SETTING Fifteen counties in southeastern Minnesota. SUBJECTS A sample of 1019 women who completed the telephone interview. MAIN OUTCOME MEASURES Self-reported Papanicolaou test, clinical breast examination, and mammography screening rates, with verification from medical records for a randomly selected subsample of 200 respondents who reported having had a test within 1 year of the interview. RESULTS For women aged 18 years and older, 60% (95% confidence interval, +/- 3.4%) reported having had a Papanicolaou test within the preceding year. For women 40 years of age and older, 57% (95% confidence interval, +/- 3.5%) reported having had a clinical breast examination in the past year, and 46% (95% confidence interval, +/- 3.6%) reported having had a screening mammogram within 1 year. The verified 1-year Papanicolaou test and mammogram rates were 35% and 33%, respectively. More than 90% of the respondents expressed a willingness to have these tests if their physicians were to advise them that the tests were indicated. However, 53% and 54% of the respondents, respectively, said that they either did not care or did not want their physicians to remind them when they were due for a Papanicolaou test or a mammogram. CONCLUSIONS Although self-reported screening rates in this population meet Healthy People 2000 goals, verified rates were significantly below target levels. A substantial proportion of women in this population remain ambivalent about participating in cancer detection programs.
Eight of Fourteen gvp Genes Are Sufficient for Formation of Gas Vesicles in Halophilic Archaea

ABSTRACT The minimal number of genes required for the formation of gas vesicles in halophilic archaea has been determined. Single genes of the 14 gvp genes present in the p-vac region on plasmid pHH1 ofHalobacterium salinarum (p-gvpACNO and p-gvpDEFGHIJKLM) were deleted, and the remaining genes were tested for the formation of gas vesicles in Haloferax volcanii transformants. The deletion of six gvp genes (p-gvpCN, p-gvpDE, and p-gvpHI) still enabled the production of gas vesicles in H. volcanii. The gas vesicles formed in some of thesegvp gene deletion transformants were altered in shape (ΔI, ΔC) or strength (ΔH) but still functioned as flotation devices. A minimal p-vac region (minvac) containing the eight remaining genes (gvpFGJKLM-gvpAO) was constructed and tested for gas vesicle formation in H. volcanii. The minvac transformants did not form gas vesicles; however, minvac/gvpJKLM double transformants contained gas vesicles seen as light refractile bodies by phase-contrast microscopy. Transcript analyses demonstrated that minvac transformants synthesized regular amounts of gvpA mRNA, but the transcripts derived from gvpFGJKLM were mainly short and encompassed onlygvpFG(J), suggesting that thegvpJKLM genes were not sufficiently expressed. SincegvpAO and gvpFGJKLM are the onlygvp genes present in minvac/JKLM transformants containing gas vesicles, these gvp genes represent the minimal set required for gas vesicle formation in halophilic archaea. Homologs of six of these gvp genes are found in Anabaena flos-aquae, and homologs of all eight minimal halobacterialgvp genes are present in Bacillus megateriumand in the genome of Streptomyces coelicolor.
G219S mutagenesis as a means of stabilizing conformational flexibility in the bacterial sodium channel NaChBac

The NaChBac sodium channel from Bacillus halodurans is a homologue of eukaryotic voltage-gated sodium channels. It can be solubilized in a range of detergents and consists of four identical subunits assembled as a tetramer. Sodium channels are relatively flexible molecules, adopting different conformations in their closed, open and inactivated states. This study aimed to design and construct a mutant version of the NaChBac protein that would insert into membranes and retain its folded conformation, but which would have enhanced stability when subjected to thermal stress. Modelling studies suggested a G219S mutant would have decreased conformational flexibility due to the removal of the glycine hinge around the proposed gating region, thereby imparting increased resistance to unfolding. The mutant expressed in Escherichia coli and purified in the detergent dodecyl maltoside was compared to wildtype NaChBac prepared in a similar manner. The mutant was incorporated into the membrane fraction and had a nearly identical secondary structure to the wildtype protein. When the thermal unfolding of the G219S mutant was examined by circular dichroism spectroscopy, it was shown to not only have a Tm ∼10°C higher than the wildtype, but also in its unfolded state it retained more ordered helical structure than did the wildtype protein. Hence the G219S mutant was shown to be, as designed, more thermally stable.
Image Quality Assessment Techniques Show Improved Training and Evaluation of Autoencoder Generative Adversarial Networks

We propose a training and evaluation approach for autoencoder Generative Adversarial Networks (GANs), specifically the Boundary Equilibrium Generative Adversarial Network (BEGAN), based on methods from the image quality assessment literature. Our approach explores a multidimensional evaluation criterion that utilizes three distance functions: an $l_1$ score, the Gradient Magnitude Similarity Mean (GMSM) score, and a chrominance score. We show that each of the different distance functions captures a slightly different set of properties in image space and, consequently, requires its own evaluation criterion to properly assess whether the relevant property has been adequately learned. We show that models using the new distance functions are able to produce better images than the original BEGAN model in predicted ways.
Granulomatous Interstitial Nephritis: A Clinicopathologic Study of 46 Cases from a Single Institution

Acute interstitial nephritis is commonly seen in kidney biopsies of patients with acute renal failure; however, granulomatous interstitial nephritis (GIN) is rare. We identified 46 cases of GIN in a 17-year period in this institution and we investigated their most probable etiologies. Complete clinical information was available in 38 patients. Seventeen of 38 patients (44.7%) were classified as drug-induced. Renal sarcoidosis was responsible for 28.9% of cases, and the remaining 15.9% of cases included Wegeners granulomatosis, foreign body giant cell reaction, GIN secondary to intravesical bacillus Calmette-Guerin therapy for bladder cancer, and xanthogranulomatous pyelonephritis. Clinical investigation failed to reveal possible etiology in 4 patients (10.5%), classified as idiopathic. We concluded that three quarters of our cases were either drug-induced or due to sarcoidosis; only a small proportion of our cases occurred secondary to any other cause or to unknown factors.
A Proteome-wide Analysis of Kinase-Substrate Network in the DNA Damage Response*

The DNA damage checkpoint, consisting of an evolutionarily conserved protein kinase cascade, controls the DNA damage response in eukaryotes. Knowledge of the in vivo substrates of the checkpoint kinases is essential toward understanding their functions. Here we used quantitative mass spectrometry to identify 53 new and 34 previously known targets of Mec1/Tel1, Rad53, and Dun1 in Saccharomyces cerevisiae. Analysis of replication protein A (RPA)-associated proteins reveals extensive physical interactions between RPA-associated proteins and Mec1/Tel1-specific substrates. Among them, multiple subunits of the chromatin remodeling complexes including ISW1, ISW2, INO80, SWR1, RSC, and SWI/SNF are identified and they undergo DNA damage-induced phosphorylation by Mec1 and Tel1. Taken together, this study greatly expands the existing knowledge of the targets of DNA damage checkpoint kinases and provides insights into the role of RPA-associated chromatins in mediating Mec1 and Tel1 substrate phosphorylation in vivo.
Financial Development and Income Inequality in Indonesia: A Sub-national Level Analysis

This study constructs financial inclusion indicator and analyzes the link of financial inclusion and income inequality for 33 provinces in Indonesia. By using Fixed Effect Panel Model, we find financial inclusion appears to have insignificant effect to on inequality at national level. While at sub-national level, adding other variables such as GRDP, years of schooling, and trade openness, we find financial inclusion appears to have negative and significant impact on income inequality in manufacture and mining-based provinces, not in agriculture-based. The results suggest that financial inclusion helps to lower income inequality when economic condition encourage people to utilize financial access for productive purposes.
Clock Auctions and Radio Spectrum Reallocation

We study the class of multiround, multiproduct clock procurement auctions that reduce offered prices at each round. When prices stop declining, the remaining bidders become the winning sellers. For single-minded bidders, each such auction has five properties not shared by Vickrey auctions: each is obviously strategy-proof and group-strategy-proof, sets prices that are Nash equilibrium winning bids in the related first-price auction, preserves winner privacy about values, and can be extended to satisfy a budget constraint. In simulations of the US incentive auction, a heuristic clock auction from this class achieves quick computations, high efficiency, and low prices.
Recognition of forked and single‐stranded DNA structures by human RAD18 complexed with RAD6B protein triggers its recruitment to stalled replication forks

Post‐replication DNA repair facilitates the resumption of DNA synthesis upon replication fork stalling at DNA damage sites. Despite the importance of RAD18 and polymerase η (Polη) for post‐replication repair (PRR), the molecular mechanisms by which these factors are recruited to stalled replication forks are not well understood. We present evidence that human RAD18 complexed with RAD6B protein preferentially binds to forked and single‐stranded DNA (ssDNA) structures, which are known to be localized at stalled replication forks. The SAP domain of RAD18 (residues 248–282) is crucial for binding of RAD18 complexed with RAD6B to DNA substrates. RAD18 mutated in the SAP domain fails to accumulate at DNA damage sites in vivo and does not guide DNA Polη to stalled replication forks. The SAP domain is also required for the efficient mono‐ubiquitination of PCNA. The SAP domain mutant fails to suppress the ultraviolet (UV)‐sensitivity of Rad18‐knockout cells. These results suggest that RAD18 complexed with RAD6B is recruited to stalled replication forks via interactions with forked DNA or long ssDNA structures, a process that is required for initiating PRR.
Aldehydes and disturbance of carbohydrate metabolism: Some consequences and possible approaches to its normalization

Abstract There are many well-documented errors of metabolism involving genetic defects that affect carbohydrate utilization. The array of disorders includes the defective utilization of glucose, as well as enzymatic deficiencies in glycolysis and gluconeogenesis, and the pentose phosphate pathway. Besides, there is considerable literature about metabolic syndrome and diabetes. However, the main problem of their origin remains obscure. Also, it is presently beyond doubt that there are various causes of insulin resistance. The development of insulin resistance may be associated not only with insulin production disorders or presence of insulin antagonists but also with modification of the number of receptors and sensitivity of peripheral tissues. The insulin resistance originates from insulin signal transmission defects at its initial stages. It is presently uncertain which mechanisms of adaptation regulation are activated or should be activated under hyperglycemia conditions. This is the main problem of the selection of strategy of hyperglycemia treatment but it is important that aldehydes—the secondary products of lipid peroxidation and protein glycation (malondialdehyde and methylglyoxal)—make a contribution to abnormal metabolism. As far as the role of methylglyoxal in inhibition of antioxidant enzymes is concerned, the involvement of the ketoaldehyde in such processes as oxidative stress, cell proliferation control, and carbohydrate metabolism disorders does not cast any doubt.
Family Relationships and Sexual Orientation Disclosure to Family by Gay and Bisexual Men in Jamaica

ABSTRACT Gay and bisexual men in Jamaica encounter stigma and discrimination due to criminalization of and negative attitudes towards same-sex sexuality. Disclosure of sexual orientation may be self-affirming, but could increase exposure to negative responses and stressors. Outcomes of an online survey among 110 gay and bisexual Jamaican men ages 18 to 56 years suggest that disclosure to family is affected by level of economic independence. Furthermore, negative familial responses to sexual identity significantly predicted depression. Social and structural interventions, and efforts to strengthen positive family relationships, are needed to foster an environment that enables well-being among sexual minorities in Jamaica.