Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.
Hitting from any direction in 3-D space by a robot with a flexible link hammer

This paper describes a hammering robot with a flexible link which can hit an object from an arbitrary direction in a 3-D space. A dynamical equation of a flexible link hammer is presented by taking gravity into consideration. The conditions that the hammer can strike an object flatwise with only a normal velocity to its face are investigated, and a manipulating method to satisfy the hitting conditions is obtained.
Experimental study of the morphology of cerebral bridging vein.

OBJECTIVE To investigate the morphological properties of pig cerebral bridging vein. METHODS The morphology and fibre arrangement of 15 cerebral bridging veins obtained from 7 Danish Yorkshire landrace pigs were observed. RESULTS There was a narrow region at the junction of the cerebral bridging veins and superior sagittal sinus termed "outflow cuff segment". The diameter and length of outflow cuff segment were much smaller and the thickness was higher than those of the cerebral bridging veins ( P < 0.01), and circumferential collagen fibres were most dense in the outflow cuff segment. The opening angle of the outflow cuff segment and the cerebral bridging veins were 115 +/- 4 degrees and 120 +/- 4 degrees ( P > 0.05). CONCLUSIONS There were differences in fibre arrangement and morphological properties between the outflow cuff segment and the cerebral bridging vein, just like a resistance valve, the outflow cuff segment may play an important role in stabilizing cerebral venous outflow and regulating intracranial pressure.
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae

We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.
Importance of left atrial appendage flow as a predictor of thromboembolic events in patients with atrial fibrillation.

AIM The purpose of this study was to investigate the role of transoesophageal echocardiography in predicting subsequent thromboembolic events in patients with atrial fibrillation. METHODS AND PATIENTS Transoesophageal echocardiography was performed in 88 patients with documented paroxysmal (n=53) or chronic atrial fibrillation (n=35) to assess morphological and functional predictors of thromboembolic events. Prospective selection was from patients with non-valvular atrial fibrillation who had undergone transoesophageal echocardiography because of previous thromboembolism (n=30); prior to electrical cardioversion (n=31); or for other reasons (n=27). All patients were followed up for 1 year. RESULTS During the period of follow-up new thromboembolic events occurred in 18 of 88 patients (20%/year); 16 of these patients had a stroke and two a peripheral embolism. Univariate analysis revealed that previous thromboembolism (P<0.005; odds ratio 5.3 [CI 1.9, 12. 1]), history of hypertension (P<0.01; odds ratio 4.0 [CI 1.4, 10.4), presence of left atrial spontaneous echo contrast (P<0.025; odds ratio 3.5 [CI 1.2, 10.0]), and presence of left atrial appendage peak velocity </=0.20 m. s-1(P<0.01; odds ratio 4.1 [CI 1.4, 11.6]) were significantly related to subsequent thromboembolic events. Stepwise logistic regression showed that independent predictors of thromboembolic events were: history of thromboembolism (P<0.005), history of hypertension (P<0.05) and low left atrial appendage peak velocity </=0.20 m. s-1(P<0.01). CONCLUSIONS In patients with atrial fibrillation, the presence of spontaneous echo contrast in the left atrium, and in particular a low left atrial appendage peak flow velocity, can be used to identify a subgroup of atrial fibrillation patients at either increased or decreased risk of subsequent thromboembolism, which might have important implications for anticoagulation therapy.
Building a multilayer macro-network for the Netherlands: A new way of looking at financial accounts and international investment position data

We argue that who-to-whom data from financial accounts can be fruitfully combined with information on the international investment position to study interconnectedness within the financial system. We illustrate this point using detailed information for the Netherlands over the year 2016. In doing so, we contribute to recent work that uses network analysis to study financial interconnectedness at the macro level. We also discuss potential further applications, such as using these network representations for financial stability analyses.
Percutaneous Needle Aspiration Biopsy (PCNA) of Pulmonary Lesions: Evaluation of a Reaspiration or a Rebiopsy (second PCNA)

Purpose: To evaluate the effectiveness of the reaspiration or rebiopsy of pulmonary lesions (second PCNA) in cases where the pathologic results are inconclusive upon initial percutaneous needle aspiration biopsy (PCNA). Materials and Methods: A total of 364 PCNA cases (350 initial PCNA, 14 second PCNA) were performed under CT or fluoroscopy guidance for all the 350 patients enrolled. The procedure was performed by either using an automated biopsy gun with a 20-G needle (298 cases) or a 20-G aspiration needle (66 cases). The pathologic agreement rates between the initial and second PCNA, as well as the causes for a second PCNA, were evaluated. Finally the type and rate of complication were also evaluated. Results: The second PCNA rate was 4.0% (14/350). The causes for a second PCNA, following the initial PCNA included unexpected pathologic results (n = 7) and inconclusive pathologic results (n = 7). Of the seven cases which had unexpected pathologic results from their initial PCNAs, five had similar pathologic results after a second PCNA. Also, of the seven cases of inconclusive pathologic results, such as atypical cells, the scanty cellularity or necrosis upon an initial PCNA, six cases revealed a malignancy on a second PCNA. The overall complication rate, including both the initial and second PCNAs was 14.0% (51/364). Conclusion: A second PCNA was performed to help resolve the exact diagnosis for a pulmonary lesion in cases of inconclusive pathologic results upon an initial PCNA.
Effects of Face Images and Face Pareidolia on Consumers' Responses to Print Advertising

ABSTRACT This research investigates whether print advertisements featuring faces (i.e., face advertisements) or facelike images (i.e., pareidolian advertisements) better capture consumer attention than advertisements that do not include such elements. In two studies, the researchers examined the effects of exposing consumers to print advertisements containing faces or pareidolian images for short time lapses—one-half, one, and three seconds. The results show that both advertisement types captured viewers' attention and more frequently were recognized than advertisements that did not feature faces or facelike objects. Both face advertisements and pareidolian advertisements increased brand recognition and advertisement preference. Theoretical and operational implications are discussed.
Coexistent axillary hydatid disease and tuberculosis: Case report of an extremely rare occurrence

Tuberculous infection is highly prevalent in India, however, hydatid disease is relatively uncommon. Frequent sites of predilection of hydatid disease are the liver and lungs. Other unusual sites of infliction are the peritoneum, thyroid, breast, pancreas, and mediastinum. Hydatid disease in the axilla is quite uncommon. We hereby report a case of coexistent axillary hydatid disease with tuberculous lymphadenitis. To the best of our knowledge, even after extensive search of the literature we did not come across any such case. Fine needle aspiration cytology (FNAC) is a cost-effective procedure performed on an outpatient basis and helped clinch a prompt diagnosis, with minimum discomfort or complications. The role of FNAC in early diagnosis cannot be overemphasized.
Cholesterol 3-Sulfate Interferes with Cornified Envelope Assembly by Diverting Transglutaminase 1 Activity from the Formation of Cross-links and Esters to the Hydrolysis of Glutamine*

The loss of transglutaminase 1 enzyme (TGase 1) activity causes lamellar ichthyosis. Recessive X-linked ichthyosis (XI) results from accumulation of excess cholesterol 3-sulfate (CSO4) in the epidermis but the pathomechanism how elevated epidermal CSO4 causes ichthyosis is largely unknown. Here we provide evidence that XI is also a consequence of TGase 1 dysfunction. TGase 1 is a key component of barrier formation in keratinocytes: it participates in the cross-linking of cell envelope (CE) structural proteins, and also forms the lipid bound envelope by esterification of long chain ω-hydroxyceramides onto CE proteins. Using involucrin and an epidermal ω-hydroxyceramide analog as substrates, kinetic analyses revealed that at membrane concentrations above 4 mol %, CSO4 caused a marked and dose-dependent inhibitory effect on isopeptide and ester bond formation. Sequencing of tryptic peptides from TGase 1-reacted involucrin showed a large increase in deamidation of substrate glutamines. We hypothesize that supraphysiological levels of CSO4 in keratinocyte membranes distort the structure of TGase 1 and facilitate the access of water into its active site causing hydrolysis of substrate glutamine residues. Our findings provide further evidence for the pivotal role of the TGase 1 enzyme in CE formation.
BENIGN PROSTATIC HYPERPLASIA ( K MCVARY , SECTION EDITOR ) Nocturia : Current Evaluation and Treatment for Urology

Nocturia is a very common yet a highly underreported entity. Recently, there has been an increasing interest in nocturia because of its association with serious adverse health conditions such as diabetes, heart disease, elevated BMI, and mortality. Frequency volume charts are the cornerstone of initial assessment and are pivotal in determining the type of nocturia and associated causes. The diagnostic evaluation is aimed at clarifying the underlying cause: sleep disturbances, reduced bladder capacity (functional or extrinsic), and increased urine production (nocturnal or daily). Obstructive sleep apnea is an important cause of nocturnal polyuria and should always been considered. Management is focused on treating the underlying cause; a range of behavioral and pharmacologic options are available.
The influence of negative publicity on brand equity: attribution, image, attitude and purchase intention

Purpose This study aims to understand the influence of negative publicity on brand image, brand attitude and brand purchase intention. Specifically, the study examines the role of attribution (or brand blame) and information characteristics in Chinese consumers’ responses to negative publicity. Design/methodology/approach The study used a quasi-experimental approach involving two negative publicity scenarios (mild and high severity) and a sample of 203 young and educated Chinese consumers. Partial least squares was used to test the hypotheses. Findings A common assumption is that negative brand information has a negative influence on all aspects of a brand. However, this study finds that brand blame and information severity have differential effects on consumer evaluations of the affected brand. Specifically, brand blame negatively impacted attitudes and purchase intentions, but not brand image. In contrast, information severity negatively impacted brand image, but not attitudes or intentions. Further, the relations between brand image and brand attitudes and intentions depended on the level of information severity. In the mild-severity condition, brand image positively influenced attitudes and intentions, but not in the high-severity condition. Research limitations/implications Future research should examine consumer responses to negative publicity across different media and product categories. Cross-cultural studies should also be explored in the future. Practical implications When a brand encounters negative publicity, its marketer or brand manager should assess to what extent various brand equity components are influenced by negative publicity before adopting any cognitive-based or imagery-based communication strategies. Originality/value This paper contributes to the limited and fragmented literature on consumer response to negative publicity by examining the impact of consumer’s attributions of blame to the brand under conditions of mild and severe negative information on a range of important brand-related outcomes. Specifically, the authors find that negative publicity has a different impact on brand image, brand attitudes and intentions to purchase. The authors suggest that brand managers use this information to guide their marketing communications.
The renal excretion of indomethacin and its inhibition by probenecid

The renal excretion of labeled indomethacin (indomethacin‐2‐C14) was measured in human volunteers with and without the concurrent administration of probenecid. Acute clearance studies provided evidence of tubular secretion of indomethacin. Less of the drug was excreted when probenecid was given. It is postulated that indomethacin is secreted by the same probenecid‐sensitive tubular mechanism as penicillin and other organic acids.
Longitudinal Growth during the First Years of Life: What Is Normal?

The anthropometric data of a longitudinal growth study on healthy infants, followed from birth until the age of 4 years and performed during 1995–1999 in The Netherlands, were used to analyze the general growth patterns in terms of height, weight and head circumference, based on z-scores, during the first 4 years of life. The well-known phenomenon where each infant or child tends to decelerate or accelerate its growth velocity depending on its starting position on the reference curve is obvious in this study too. This phenomenon, known as the regression to the mean, is a strong phenomenon especially during the first year. Regression to the mean is calculated for the different age groups as factor. With the given α, it is possible to estimate the individual expectation of growth.
HLA association and occurrence of autoantibodies in Asian-Indian patients with ulcerative colitis.

OBJECTIVES The purpose of the present study was to determine the profile of HLA class I antigens, antinuclear antibodies (ANA), and antineutrophil cytoplasmic antibodies (ANCA) in ulcerative colitis (UC) patients from Northern India. METHODS The study consisted of 100 UC patients with or without extraintestinal manifestations. Data on HLA, ANA, and ANCA were analyzed with respect to age at onset, sex, duration of disease, and occurrence of extraintestinal manifestations, and data were correlated with those of healthy controls from the same population. RESULTS The most common extraintestinal manifestations in order of occurrence were arthralgia (53.8%), ocular lesions (18%), sacroiliitis (12.7%), hepatobiliary (7.7%), cutaneous (5%), and vascular (2.6%). ANA and ANCA were positive in only 3% of cases. Of the HLA class I antigens, HLA-A19 was significantly increased in UC patients compared with controls (63.4% vs. 33.5%, p < 0.001, RR = 3.4), particularly its subtype HLA-A33 (20.7% vs. 4%, p < 0.001, RR = 6.3). There was no deviation in the frequency of HLA-B locus antigens, whereas HLA-Cw6 was increased significantly in patients compared with controls (14.6% vs. 3.5%, p < 0.001, RR = 4.4). CONCLUSIONS The occurrence of extraintestinal manifestations in Indian patients with UC is similar to that reported elsewhere, although ANA and ANCA positivity is lower. HLA studies revealed that A19(33) and Cw6 are associated with UC.
Anesthesia for Cardiac Transplantation: A Practical Overview of Current Management Strategies

Although being a standard surgical procedure since decades, heart transplantation remains a challenge for the cardiac anesthetist as it requires a sophisticated monitoring and management of circulation, ventilation and homeostasis. Right ventricular failure is the main contributor to early graft failure in heart transplantation. Particularly after prolonged ischemia and reperfusion injury, the donor heart often can not easily adapt to the increased pulmonary artery pressure and pulmonary vascular resistance of the recipient. Therefore, the special task of anesthesia for heart transplantation is to measure and calculate the actual pressures, resistance and transpulmonary gradient in the pulmonary artery bed of the recipient, initiate strategies to reduce pulmonary artery pressure and resistance and to augment right ventricular contractility. After induction of anesthesia and placement of monitoring lines, a pulmonary artery catheter should be forwarded into the pulmonary artery and measurements performed.These data give important information in how far the patient will be at risk for an increased afterload of the right ventricle and concomitant right ventricular failure. Besides basic ventilation strategies to reduce pulmonary artery resistance such as hyperoxygenation and moderate hyperventilation are compulsory. Inhalation of selective pulmonary artery vasodilators such as nitric oxide or aerosolized prostaglandins should be initiated in case of an increased pulmonary artery pressure and resistance. Inotropic support of the right ventricle is achieved by a combination of beta-adrenergic drugs and phosphodiesterase-3 inhibitors. The effect of the therapy is monitored by measurement of cardiac output, left and right atrial filling pressures and pulmonary artery pressures and continuous monitoring of right and left ventricular function by online transesophageal echocardiography. If the left ventricular preload remains unsatisfactory during this therapy, a vasoconstrictor should be infused to achieve adequate systemic arterial (diastolic) pressures providing adequate coronary artery perfusion. If even these strategies fail to achieve adequate cardiac output the calcium channel sensitizer levosimendan and/or replacement of triiodthyronine (T3), which plasma levels are often decreased during longer periods of cardiopulmonary bypass, are additional pharmacological options. If pharmacological therapy remains unsatisfying to establish a stable circulatory condition, mechanical support must be established. Severe hemorrhage is not a rare condition especially in patients with previous heart surgery and will be managed with replacement of coagulation factor concentrates and/or infusion of fresh frozen plasma and transfusion of platelet concentrates. Current monitoring assays such as the ROTEM device help to guide specific therapy. In case of uncontrollable hemorrhage infusion of recombinant coagulation factor VIIa is an ultimate option.
Clinical and economic outcomes – friend or foe?

The growing interest in analyzing the cost-effectiveness of interventions presents a challenge to anyone involved in dementia research. Although not yet often expressed as a formal requirement, drug authorities and budget holders also wish to have information on cost effectiveness. Clinical outcomes must therefore be combined with outcomes suitable for cost effectiveness analysis. However, issues about cost effectiveness are seldom included in empirical clinical trials, but are more often analyzed using modeling approaches. Clinical researchers and economists need to bridge these areas of potential conflict when long-term cost effectiveness is being considered. Randomized clinical trials (RCTs), observational studies, register data and economic models all have their advant-ages and drawbacks, and in making statements about cost effectiveness it is necessary to make a comprehensive judgment based on several methodological approaches. RCTs with a duration of at least 12 months should include assess-ments of resource utilization, and outcomes should offer a link to population-based cohort studies to discuss generalizability (e.g. a cognitive measure avail-able both in trials and cohort studies, such as the Mini-mental State Examination (MMSE), staging instruments, quality of life instruments) of the costs, while also serving as one source of modeling. Both dementia-specific and generic quality of life instruments are required. Models are necessary but must be transparent so that the assumptions on which the models are built can be critically analyzed.