tbuckley/cabot-search huggingface dataset:
Centromeres Off the Hook: Massive Changes in Centromere Size and Structure Following Duplication of<i>CenH3</i>Gene in<i>Fabeae</i>Species
Authors: Pavel Neumann, Zuzana Pavlíková, Andrea Koblížková, Iva Fuková, Veronika Jedličková, Petr Novák, Jiří Macas
Journal: Molecular Biology and Evolution (2015)

In most eukaryotes, centromere is determined by the presence of the centromere-specific histone variant CenH3. Two types of chromosome morphology are generally recognized with respect to centromere organization. Monocentric chromosomes possess a single CenH3-containing domain in primary constriction, whereas holocentric chromosomes lack the primary constriction and display dispersed distribution of CenH3. Recently, metapolycentric chromosomes have been reported in Pisum sativum, representing an intermediate type of centromere organization characterized by multiple CenH3-containing domains distributed across large parts of chromosomes that still form a single constriction. In this work, we show that this type of centromere is also found in other Pisum and closely related Lathyrus species, whereas Vicia and Lens genera, which belong to the same legume tribe Fabeae, possess only monocentric chromosomes. We observed extensive variability in the size of primary constriction and the arrangement of CenH3 domains both between and within individual Pisum and Lathyrus species, with no obvious correlation to genome or chromosome size. Search for CenH3 gene sequences revealed two paralogous variants, CenH3-1 and CenH3-2, which originated from a duplication event in the common ancestor of Fabeae species. The CenH3-1 gene was subsequently lost or silenced in the lineage leading to Vicia and Lens, whereas both genes are retained in Pisum and Lathyrus. Both of these genes appear to have evolved under purifying selection and produce functional CenH3 proteins which are fully colocalized. The findings described here provide the first evidence for a highly dynamic centromere structure within a group of closely related species, challenging previous concepts of centromere evolution.
Diagnostic principles in pleural disease
Authors: RW Light
Journal: European Respiratory Journal (1997)

When a patient with an undiagnosed pleural effusion is evaluated, the first question to answer is whether the patient has a transudate or an exudate. This is best done using Light's criteria, but these criteria occasionally misidentify a transudate as an exudate. If the patient's pleural fluid meets exudative criteria, but the patient appears clinically to have a transudative effusion, then the serum-pleural fluid albumin gradient should be measured. If this is greater than 1.2 g-dL-1, the patient probably does have a transudative effusion. If the patient has an exudative pleural effusion, additional tests are indicated to determine the aetiology of the effusion. The gross appearance and the odour of the pleural fluid should be noted and samples of all exudates should be sent for bacterial cultures. Laboratory tests that are useful in the differential diagnosis of exudative pleural effusions include: differential white cell count of the pleural fluid; cytology of the pleural fluid; and levels of adenosine deaminase, glucose, amylase and lactate dehydrogenase in the pleural fluid. If pleural tuberculosis is suspected, a needle biopsy of the pleura is indicated. Thoracoscopy is very efficient at diagnosing malignant pleural effusion and tuberculosis pleuritis, but rarely establishes any other diagnosis.
Lifetime Risks of Cardiovascular Disease
Authors: Jarett D. Berry, Alan Dyer, Xuan Cai, Daniel B. Garside, Hongyan Ning, Avis Thomas, Philip Greenland, Linda Van Horn, Russell P. Tracy, Donald M. Lloyd-Jones
Journal: New England Journal of Medicine (2012)

The lifetime risks of cardiovascular disease have not been reported across the age spectrum in black adults and white adults.
Genetic variations of Toll-like receptor 9 predispose to systemic lupus erythematosus in Japanese population
Authors: K. Tao, M. Fujii, S.-i. Tsukumo, Y. Maekawa, K. Kishihara, Y. Kimoto, T. Horiuchi, H. Hisaeda, S. Akira, S. Kagami, K. Yasutomo
Journal: Annals of the Rheumatic Diseases (2007)

Systemic lupus erythematosus (SLE) is characterised by dysregulation of autoreactive lymphocytes and antigen-presenting cells. Signalling through Toll-like receptor 9 (TLR9), a mediator of innate immune responses, has a role in activation of dendritic cells and autoreactive B cells.To investigate whether TLR9 polymorphisms are associated with an increased risk of SLE.DNA samples were obtained from 220 Japanese patients with SLE (with >4 American College of Rheumatology criteria for SLE) and 203 controls. The genetic variations of TLR9 were detected by PCR, followed by DNA sequencing. The promoter and enhancer activities of TLR9 were measured by luciferase reporter gene assay. The titres of anti-dsDNA antibodies in sera from control or TLR9-deficient mice were analysed by ELISA.The G allele at position +1174 (located in intron 1 of TLR9) is closely associated with an increased risk of SLE (p = 0.029). Furthermore, patients with SLE tend to have C allele at position -1486 (p = 0.11). Both alleles down regulate TLR9 expression by reporter gene assay. TLR9-deficient mice under a C57BL/6 background possess higher titres of anti-dsDNA serum antibodies than control C57BL/6 mice.These results indicate that the presence of the G allele at position +1174 of TLR9 predisposes humans to an increased risk of SLE. It is speculated that TLR9 normally prevents the development of human SLE.
Total body water and total body potassium in patients with continent ileostomies.
Authors: L O Nilsson, H Andersson, I Bosaeus, H E Myrvold
Journal: Gut (1982)

<h3>Abstract</h3> CITE-seq technology enables the direct measurement of protein expression, known as antibody-derived tags (ADT), in addition to RNA expression. The increase in the copy number of protein molecules leads to a more robust detection of protein features compared to RNA, providing a deep definition of cell types. However, due to added discrepancies of antibodies, such as the different types or concentrations of IgG antibodies, the batch effects of the ADT component of CITE-seq can dominate over biological variations, especially for the across-study integration. We present ADTnorm as a normalization and integration method designed explicitly for the ADT counts of CITE-seq data. Benchmarking with existing scaling and normalization methods, ADTnorm achieves a fast and accurate matching of the negative and positive peaks of the ADT counts across samples, efficiently removing technical variations across batches. Further quantitative evaluations confirm that ADTnorm achieves the best cell-type separation while maintaining the minimal batch effect. Therefore, ADTnorm facilitates the scalable ADT count integration of massive public CITE-seq datasets with distinguished experimental designs, which are essential for creating a corpus of well-annotated single-cell data with deep and standardized annotations. <h3>Contact</h3> raphael.gottardo@chuv.ch <h3>Supplementary information</h3> Supplementary data are available online.
Robot-Assisted Therapy for Long-Term Upper-Limb Impairment after Stroke
Authors: Albert C. Lo, Peter D. Guarino, Lorie G. Richards, Jodie K. Haselkorn, George F. Wittenberg, Daniel G. Federman, Robert J. Ringer, Todd H. Wagner, Hermano I. Krebs, Bruce T. Volpe, Christopher T. Bever, Dawn M. Bravata, Pamela W. Duncan, Barbara H. Corn, Alysia D. Maffucci, Stephen E. Nadeau, Susan S. Conroy, Janet M. Powell, Grant D. Huang, Peter Peduzzi
Journal: New England Journal of Medicine (2010)

Effective rehabilitative therapies are needed for patients with long-term deficits after stroke.In this multicenter, randomized, controlled trial involving 127 patients with moderate-to-severe upper-limb impairment 6 months or more after a stroke, we randomly assigned 49 patients to receive intensive robot-assisted therapy, 50 to receive intensive comparison therapy, and 28 to receive usual care. Therapy consisted of 36 1-hour sessions over a period of 12 weeks. The primary outcome was a change in motor function, as measured on the Fugl-Meyer Assessment of Sensorimotor Recovery after Stroke, at 12 weeks. Secondary outcomes were scores on the Wolf Motor Function Test and the Stroke Impact Scale. Secondary analyses assessed the treatment effect at 36 weeks.At 12 weeks, the mean Fugl-Meyer score for patients receiving robot-assisted therapy was better than that for patients receiving usual care (difference, 2.17 points; 95% confidence interval [CI], -0.23 to 4.58) and worse than that for patients receiving intensive comparison therapy (difference, -0.14 points; 95% CI, -2.94 to 2.65), but the differences were not significant. The results on the Stroke Impact Scale were significantly better for patients receiving robot-assisted therapy than for those receiving usual care (difference, 7.64 points; 95% CI, 2.03 to 13.24). No other treatment comparisons were significant at 12 weeks. Secondary analyses showed that at 36 weeks, robot-assisted therapy significantly improved the Fugl-Meyer score (difference, 2.88 points; 95% CI, 0.57 to 5.18) and the time on the Wolf Motor Function Test (difference, -8.10 seconds; 95% CI, -13.61 to -2.60) as compared with usual care but not with intensive therapy. No serious adverse events were reported.In patients with long-term upper-limb deficits after stroke, robot-assisted therapy did not significantly improve motor function at 12 weeks, as compared with usual care or intensive therapy. In secondary analyses, robot-assisted therapy improved outcomes over 36 weeks as compared with usual care but not with intensive therapy. (ClinicalTrials.gov number, NCT00372411.)
Are HIV Epidemics among Men Who Have Sex with Men Emerging in the Middle East and North Africa?: A Systematic Review and Data Synthesis
Authors: Ghina Mumtaz, Nahla Hilmi, Willi McFarland, Rachel L. Kaplan, Francisca Ayodeji Akala, Iris Semini, Gabriele Riedner, Oussama Tawil, David Wilson, Laith J. Abu-Raddad
Journal: PLoS Medicine (2011)

Background Men who have sex with men (MSM) bear a disproportionately higher burden of HIV infection than the general population. MSM in the Middle East and North Africa (MENA) are a largely hidden population because of a prevailing stigma towards this type of sexual behavior, thereby limiting the ability to assess infection transmission patterns among them. It is widely perceived that data are virtually nonexistent on MSM and HIV in this region. The objective of this review was to delineate, for the first time, the evidence on the epidemiology of HIV among MSM in MENA. Methods and Findings This was a systematic review of all biological, behavioral, and other related data on HIV and MSM in MENA. Sources of data included PubMed (Medline), international organizations' reports and databases, country-level reports and databases including governmental and nongovernmental organization publications, and various other institutional documents. This review showed that onsiderable data are available on MSM and HIV in MENA. While HIV prevalence continues at low levels among different MSM groups, HIV epidemics appear to be emerging in at least few countries, with a prevalence reaching up to 28% among certain MSM groups. By 2008, the contribution of MSM transmission to the total HIV notified cases increased and exceeded 25% in several countries. The high levels of risk behavior (4–14 partners on average in the last six months among different MSM populations) and of biomarkers of risks (such as herpes simplex virus type 2 at 3%–54%), the overall low rate of consistent condom use (generally below 25%), the relative frequency of male sex work (20%–76%), and the substantial overlap with heterosexual risk behavior and injecting drug use suggest potential for further spread. Conclusions This systematic review and data synthesis indicate that HIV epidemics appear to be emerging among MSM in at least a few MENA countries and could already be in a concentrated state among several MSM groups. There is an urgent need to expand HIV surveillance and access to HIV testing, prevention, and treatment services in a rapidly narrowing window of opportunity to prevent the worst of HIV transmission among MSM in the Middle East and North Africa. Please see later in the article for the Editors' Summary
Evidence-Based Cardiology in Hemodialysis Patients
Authors: Michael Allon
Journal: Journal of the American Society of Nephrology (2013)

Cardiac events are the major cause of death in hemodialysis patients. Because of the paucity of randomized clinical trials (RCTs) in hemodialysis patients, most cardiovascular therapies in this population are based on observational studies or results extrapolated from studies that excluded hemodialysis patients. However, associations discovered in observational studies do not prove causality, and these studies often report surrogate outcomes rather than clinical end points. Furthermore, interventions that show effectiveness in the general population may have drastically different outcomes and side effect profiles in hemodialysis patients. This review discusses the results of RCTs undertaken recently to evaluate cardiovascular therapies in hemodialysis patients and emphasizes clinically relevant outcomes. Although some interventions have produced similar outcomes in hemodialysis patients and the general population, others have not, suggesting that the management of cardiovascular disease in hemodialysis patients may require strategies that differ from the best practice guidelines applied to general population.
Epidemiology of chronic Pseudomonas aeruginosa infections in the airways of lung transplant recipients with cystic fibrosis
Authors: S. Walter, P. Gudowius, J. Bosshammer, U. Romling, H. Weissbrodt, W. Schurmann, H. von der Hardt, B. Tummler
Journal: Thorax (1997)

BACKGROUND: The source of airway colonisation with Pseudomonas aeruginosa is not well defined in patients with cystic fibrosis after lung transplantation. Using a DNA-based typing system a study was undertaken to investigate whether lung transplant recipients acquired new strains of P aeruginosa or retained those they had before transplantation. METHODS: Seventy four P aeruginosa isolates taken before and after transplantation were analysed from 11 patients with cystic fibrosis who had undergone lung transplantation in the Medical School of Hannover between 1988 and 1994. The genetic relatedness of the 74 P aeruginosa strains was evaluated from macrorestriction fragment pattern similarity. RESULTS: Each of the 11 lung transplant recipients harboured one identical P aeruginosa clone before and after transplantation. The airways of four of the 11 patients were preoperatively colonised by two or three different clones, but six months after transplantation only one clone was detectable. CONCLUSIONS: These results show that there is no change in the P aeruginosa population in the airways of lung transplant recipients before and after transplantation and it is assumed that the chronic drainage of P aeruginosa into the lung allografts is caused by the bacterial reservoir in the paranasal sinuses and the trachea.
Decreased Affinity of Blood for Oxygen in Patients with Low-Output Heart Failure
Authors: JAMES METCALFE, DHARAM S. DHINDSA, MILES J. EDWARDS, ATHANASIOS MOURDJINIS
Journal: Circulation Research (1969)

Oxygen affinity of blood was measured in 16 patients (nonsmokers) without anemia and with clinical evidence of low cardiac output. Of these patients, 12 were catheterized and showed an arteriovenous oxygen concentration difference across the lungs greater than 5 ml/100 ml. The partial pressure of oxygen required to half-saturate their blood with oxygen (P 50 ) averaged 29.4 mm Hg (SD ± 1.9). Blood from normal subjects (nonsmokers) had an average P 50 of 27.3 mm Hg (SD ± 0.9). The decreased oxygen affinity found in blood of patients with low levels of cardiac output is considered as a compensatory adjustment to poor tissue blood flow, promoting the diffusion of oxygen from blood in tissue capillaries to intracellular sites of utilizaton.
Factors Associated with Improvement in Deceased Donor Renal Allograft Function in the 1990s
Authors: Douglas S. Keith, Angelo deMattos, Muralikrishna Golconda, Jonathan Prather, Marcelo Cantarovich, Steven Paraskevas, Jean Tchervenkov, Douglas J. Norman
Journal: Journal of the American Society of Nephrology (2005)

The decade of the 1990s saw an improvement in cadaveric renal graft function and dramatic reduction in the acute rejection (AR) rate. The purpose of this study was to determine whether the reduction in rejection rate was the primary cause of the improvement in graft function seen and whether this improved long-term graft survival. All adult patients who received a cadaver renal transplant between 1991 and 2000 and had graft survival of at least 6 mo and complete data for creatinine at 6 mo, HLA mismatch, delayed graft function, and acute rejection (AR) were identified in the United Network for Organ Sharing database. A total of 40,164 cases that met the inclusion criteria were identified. The mean Modification of Diet in Renal Disease GFR at 6 mo improved from 49.94 ml/min per 1.73 m2 in 1991 to 54.59 ml/min per 1.73 m2 in 2000 (P < 0.001). The improvement in GFR was not gradual but occurred over a 4-yr period between 1994 and 1997, coinciding with the introduction of new immunosuppressive agents mycophenolate mofetil and tacrolimus into maintenance immunosuppression regimens. The improvement was seen in all subgroups of patients, even patients without clinical AR or delayed graft function. The magnitude of improvement in patients without clinical AR was similar to that seen in patients with AR. The drop in clinical AR rate accounted for a minority of the improvement in graft function in the 1990s. Other factors, such as reduced drug toxicity and improved control of subclinical rejection, seem to account for the majority of the improvement. This improvement in graft function at 6 mo did not translate into improved long-term graft survival, however.
Antiidiotypic DNA vaccination induces serum bactericidal activity and protection against group B meningococci
Authors: Concetta Beninati, Angelina Midiri, Giuseppe Mancuso, Carmelo Biondo, Milena Arigò, Elisabetta Gerace, Salvatore Papasergi, Maria Gambuzza, Mauro Boretti, Walter Magliani, Stefania Conti, Luciano Polonelli, Giuseppe Teti
Journal: The Journal of Experimental Medicine (2006)

No vaccine is available for preventing infections by serogroup B Neisseria meningitidis (MenB), which accounts for a major portion of meningococcal cases in developed countries, because of the poor immunogenicity of the capsular polysaccharide (CP) even after protein conjugation. We have previously induced anticapsular antibodies by immunization with a single chain variable fragment (scFv), which mimics a protective CP epitope. This surrogate antigen, however, was ineffective at inducing serum bactericidal activity, an accepted marker of protection in humans. Serum bactericidal activity was consistently achieved by immunizing mice with the scFv-encoding gene. Immunization with vectors without a secretory signal sequence before the scFv resulted in markedly higher bactericidal activity relative to those with such a sequence. The induced antibodies were capsule specific, as shown by complete inhibition of bactericidal activity by purified MenB CP and by resistance to killing of MenA or MenC. Moreover, these antibodies were predominantly of the IgG2a isotype, reflecting a T helper type 1 response. Administration of sera from scFv gene–vaccinated animals protected infant rats against MenB bacteremia. These data illustrate the potential of vaccination with genes encoding capsular mimics in providing protection against MenB and other encapsulated bacteria.
Comprehensive Follow-up Care and Life-Threatening Illnesses Among High-Risk Infants
Authors: R. Sue Broyles, Jon E. Tyson, Elizabeth T. Heyne, Roy J. Heyne, Jackie F. Hickman, Michael Swint, Sally S. Adams, Linda A. West, Nancy Pomeroy, Patricia J. Hicks, Chul Ahn
Journal: JAMA (2000)

EONATAL FOLLOW-UP PROgrams were originally developed to survey the outcome of high-risk infants, assess the effects of perinatal insults and care, and identify infants needing referral for care of ongoing problems.Unfortunately, this approach has often been associated with a substantial loss to follow-up among families of lower socioeconomic status. 1,2Moreover, this approach does not address the needs of very-low-birth-weight infants of any socioeconomic situation who lack access to a physician skilled in managing the pulmonary, gastrointestinal, nutritional, neurological, developmental, and other problems common among these infants. 1-5Some follow-up programs now provide well-baby care and care for chronic illnesses.However, care for acute illnesses typically is not pro-vided.Without prompt, effective treatment, minor illnesses or complications may quickly become lifethreatening in these vulnerable infants.This problem is likely to contribute to their increased mortality, morbidity, and cost of care throughout infancy.
Treatment of Broncho-Pulmonary Suppuration by Local Injection of Penicillin: Report of 63 Cases
Authors: H. Metras, J. Lieutier
Journal: Thorax (1947)

After using Thomson's catheter for bronchography one of us designed a set of special radio-opaque rubber catheters (Figs. 1 and2) which allow the injection of radio-opaque substances not only into a lobe but even into separate and selected broncho-pulmonary segments.A sound knowledge of the aliatomy of the bronchial tree is essential in order to perform selective placing of the catheter, and this knowledge may be acquired by studying the French and American literature and from the book recently written by Brock (1946).After we had used the special catheters for bronchography it occurred to us to use them also for injecting penicillin directly into a lung abscess by way of the natural route, namely the tracheo-bronchial tree.At first sight the procedure seems illogical, but an earlier study of the behaviour of radio-opaque fluids in the bronchial tree had shown us that it is possible to inject fluids with suitable physical characters into a diseased area.Lipiodol, which is a viscous fluid, spreads throughout the bronchi, if they are normal, chiefly by aspiration on inspiration.Thus if a catheter is placed in the upper lobe bronchus the lipiodol will reach the bronchioli of the apical segment even if the patient remains erect.If, however, this segment is diseased or im- perfectly aerated, and especially if the bronchi are slightly narrowed or obstructed, such a viscous fluid will not pass beyond the larger bronchi.On the other hand, if less viscous oil be used this will run down the bronchi and, aided by gravity, will pass through narrowed bronchi provided these are directed vertically down- wards.Thus, if a catheter be placed at the orifice of the bronchus draining a selected segment and the patient be placed so that this segment is dependent, fluid of low viscosity will flood only this one segment.In the same way an aqueous solution of penicillin can be directed into a selected broncho-pulmonary segment provided the bronchus is catheterized and the patient placed in the appropriately favourable position.Several workers have shown that penicillin acts more powerfully if placed directly into the area of suppuration instead of being given systemically.This is true in the case of the brain, pleura, and bones, and we hope to show that it is also true for the lungs.
Mental attention, not language, may explain evolutionary growth of human intelligence and brain size
Authors: Juan Pascual-Leone
Journal: Behavioral and Brain Sciences (2006)

Using neoPiagetian theory of mental attention (or working memory), I task-analyze two complex performances of great apes and one symbolic performance (funeral burials) of early Homo sapiens . Relating results to brain size growth data, I derive estimates of mental attention for great apes, Homo erectus , Neanderthals, and modern Homo sapiens , and use children's cognitive development as reference. This heuristic model seems consistent with research.