tbuckley/cabot-search huggingface dataset:
Linear correlates in the speech signal: The orderly output constraint
Authors: Harvey M. Sussman, David Fruchter, Jon Hilbert, Joseph Sirosh
Journal: Behavioral and Brain Sciences (1998)

Neuroethological investigations of mammalian and avian auditory systems have documented species-specific specializations for processing complex acoustic signals that could, if viewed in abstract terms, have an intriguing and striking relevance for human speech sound categorization and representation. Each species forms biologically relevant categories based on combinatorial analysis of information-bearing parameters within the complex input signal. This target article uses known neural models from the mustached bat and barn owl to develop, by analogy, a conceptualization of human processing of consonant plus vowel sequences that offers a partial solution to the noninvariance dilemma – the nontransparent relationship between the acoustic waveform and the phonetic segment. Critical input sound parameters used to establish species-specific categories in the mustached bat and barn owl exhibit high correlation and linearity due to physical laws. A cue long known to be relevant to the perception of stop place of articulation is the second formant (F2) transition. This article describes an empirical phenomenon – the locus equations – that describes the relationship between the F2 of a vowel and the F2 measured at the onset of a consonant-vowel (CV) transition. These variables, F2 onset and F2 vowel within a given place category, are consistently and robustly linearly correlated across diverse speakers and languages, and even under perturbation conditions as imposed by bite blocks. A functional role for this category-level extreme correlation and linearity (the “orderly output constraint”) is hypothesized based on the notion of an evolutionarily conserved auditory-processing strategy. High correlation and linearity between critical parameters in the speech signal that help to cue place of articulation categories might have evolved to satisfy a preadaptation by mammalian auditory systems for representing tightly correlated, linearly related components of acoustic signals.
GENCODE: producing a reference annotation for ENCODE
Authors: Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao-Kung Chen, Jacqueline Chrast, Julien Lagarde, James GR Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos E Antonarakis, Roderic Guigo
Journal: Genome biology (2006)

The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions.In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.
Increased Adiposity at Diagnosis in Younger Children With Type 1 Diabetes Does Not Persist
Authors: Samantha L. Clarke, Maria E. Craig, Sarah P. Garnett, Albert K. Chan, Christopher T. Cowell, Janine M. Cusumano, Olga Kordonouri, Abi Sambasivan, Kim C. Donaghue
Journal: Diabetes Care (2006)

Increased adiposity, as measured by BMI, has been described in younger children at diagnosis of type 1 diabetes compared with older children (1–3) in support of the “accelerator hypothesis” (1). Australia has one of the highest rates of childhood obesity in the Western world, but a disproportionate increase in type 1 diabetes incidence has not been observed in young children (4), which is contrary to recent reports of other populations (5,6). We therefore sought to investigate whether anthropometric data at diagnosis from 1976 to 2004 support the accelerator hypothesis in our population.

In addition to its potential contribution to type 1 diabetes etiology, the insulin resistance associated with increased adiposity places these children at greater risk of vascular disease (7–9). In a cross-sectional study of children with median diabetes duration of 3 years, we have previously found that those with the highest BMI SD score (SDS) were younger and had worse metabolic control (10). Hence, in this longitudinal study, we examined whether increased adiposity at diagnosis persisted in the youngest children after 5 years.

The study group consisted of children and adolescents attending the diabetes outpatient and outreach clinics of the Royal Alexandra Hospital for Children in Sydney and rural New South Wales, Australia, from 1976 to 2004. To exclude the initial weight loss due to acute destabilization, only height, weight, and BMI available 1–3 months postdiagnosis were analyzed ( n = 960). In those diagnosed …
Now do it our way
Authors: N. Goodman
Journal: Journal of the Royal Society of Medicine (2005)

Some years ago, my hospital and the neighbouring one became a single Trust.It was clear from the outset that we could not provide proper health care to our population until the Trust became a single hospital.Commissions were set up and outline business cases were prepared.Outside consultants-not of the medical sort-were employed.Committees were formed, people met, and options were suggested.Reams of documents appeared, some on watermarked paper expensively bound.There were public consultation exercises, and the public service unions had their say.The plurals are important here, because the rigmarole was gone through at least three times.Each time, the process came to a halt.Whatever other factors were important, there was political foot-dragging by whichever set of politicians was going to lose 'their' hospital.But the medical staff carried on with their plans, hoping that eventually the ineluctable logic of the situation would get through even the thickest political skull.The considered options at the latest exercise were the same as considered by each of the previous commissions: status quo (rejected on every occasion), on our site, on their site, new site.The European Working Time Directive was the final evidence we needed to persuade local politicians that a new build was the only sensible answer to our continuing health care problems.Individually and collectively the politicians were canvassed, and at last the argument seemed won.They agreed, some of them reluctantly, but none the less they agreed.There was little to choose between our site and their site, but our site won by a bit more than a nose.The medical staff came out in favour.We were going to get our new hospital-not until 2012 at the soonest, but it was on its way.At last, we could plan properly.I sat on committees where we talked about how many operating theatres there would be, how many anaesthetists it would need, how the day case unit would relate to the main theatre suite.The medical director went to the USA to look at the layout of large hospitals and consider which would work best for us.A meeting was planned for the architects to talk to the senior medical staff at the medical advisory committee about details of where we would be working, and whose office or clinic would be next door.The meeting was planned for August.Complaints flooded in about the holiday season: the meeting was postponed.
Understanding Research Synthesis (Meta-Analysis)
Authors: Frederick Mosteller, Graham A. Colditz
Journal: Annual Review of Public Health (1996)

Synthesis of research findings has long been a part of reviewing and summarizing a field of study. Public health decisions are made on the available evidence. We summarize the approaches to research synthesis that draw on the best available evidence and the use of quantitative summaries through meta-analysis. We focus on observational studies. Heterogeneity offers the potential to observe a relation across study populations and circumstances. We emphasize the benefits of heterogeneity in overviews and the need to explore and describe the sources of heterogeneity. Random effects approaches to combining data are recommended, and the use of regression approaches is emphasized. Excluding studies with extreme results may bias a research synthesis and underestimate the true variance of the results, thus contributing to misleading inference. Thorough searching is the best guard against publication bias. We conclude with guidelines for combining epidemiological studies.
Evaluation of the intrinsic innervation of the internal anal sphincter using electrical stimulation.
Authors: M A Kamm, J E Lennard-Jones, R J Nicholls
Journal: Gut (1989)

Stimulation of the rectal mucosa with a bipolar electrode leads to relaxation of the internal anal sphincter. Intraoperative studies in two subjects showed that transmission of the impulse was independent of extrinsic nerves and was interrupted by circular myotomy. Characteristics of the reflex were studied in 11 healthy women and 19 women with severe idiopathic constipation. One control subject and two patients did not tolerate the test. In the remainder the stimulus caused a clearly defined fall in internal sphincter pressure. The mean resting maximum anal canal pressure before stimulation was the same in both groups (90 (10) v 104 (7) cm H2O, p = 0.3, controls v patients). The threshold stimulus for relaxation (12 (2) v 14 (1) mamps, p = 0.5), the maximum percent fall in resting pressure (43 (7) v 46 (4)%, p = 0.7) and the lowest absolute resting pressure produced by stimulation (48 (13) v 49 (6) cm H2O, p = 0.9) were the same in both groups. The stimulus required to achieve maximum relaxation was significantly higher in the patient group (23 (3) v 32 (2) mamps, p = 0.012) suggesting abnormal intrinsic innervation of the sphincter in these patients. Electrical stimulation should not replace balloon distension for routine testing of the rectoanal reflex but it may be useful in quantitative studies.
Psychiatric Aspects of Klinefelter's Syndrome
Authors: DAVID W. SWANSON, ALBERT H. STIPES
Journal: American Journal of Psychiatry (1969)

Klinefelter's syndrome is a chromosomal abnormality resulting in hypogonadism. Intellectual impairment and/or neuropsychiatric disorder are present in many cases. The variety of psychopathology accompanying the syndrome is reviewed from the literature and by case reports. The typical individual has a generalized inability to adapt, low social drive, lack of exploratory behavior, and emotional instability. He may also manifest a variety of neurotic, psychotic, and sociopathic behaviors that appear to be compensatory and individual in character.
Cocaine induced eosinophilic lung disease.
Authors: P I Oh, M S Balter
Journal: Thorax (1992)

A patient developed fever, bronchoconstriction, hypoxaemia, pulmonary infiltrates, and serum and bronchoalveolar lavage fluid eosinophilia on two occasions after inhaling crack cocaine. Transbronchial biopsy specimens showed normal lung parenchyma but a dense eosinophilic infiltrate within the bronchial wall. Both episodes resolved promptly after treatment with corticosteroids. Eosinophilic lung disease may be a steroid responsive complication of crack cocaine abuse.
PML-RAR induces promyelocytic leukemias with high efficiency following retroviral gene transfer into purified murine hematopoietic progenitors
Authors: Saverio Minucci, Silvia Monestiroli, Sabrina Giavara, Simona Ronzoni, Francesco Marchesi, Alessandra Insinga, Daniela Diverio, Patrizia Gasparini, Manuela Capillo, Emanuela Colombo, Cristian Matteucci, Francesco Contegno, Francesco Lo-Coco, Eugenio Scanziani, Alberto Gobbi, Pier Giuseppe Pelicci
Journal: Blood (2002)
Elimination of early rehospitalization in a randomized, controlled trial of multidisciplinary care in a high‐risk, elderly heart failure population: the potential contributions of specialist care, clinical stability and optimal angiotensin‐converting enzyme inhibitor dose at discharge
Authors: Kenneth McDonald, Mark Ledwidge, John Cahill, Jean Kelly, Peter Quigley, Brian Maurer, Fiona Begley, Mary Ryder, Bronagh Travers, Lorna Timmons, Teresa Burke
Journal: European Journal of Heart Failure (2001)
Cost of tuberculosis in the era of multidrug resistance: will it become unaffordable?
Authors: Robert Loddenkemper, Giovanni Sotgiu, Carole D. Mitnick
Journal: European Respiratory Journal (2012)

In 1905, Robert Koch ended his Nobel Lecture on “The current state of the struggle against tuberculosis” with the optimistic sentence: “If the work goes on in this powerful way, then the victory must be won” [1]. At the end of the 1970s and the beginning of the 1980s, many believed that tuberculosis (TB) was nearly vanquished [2]. Now, more than 100 years after Koch’s Nobel Lecture, TB has emerged as an even greater public health problem, mainly for two reasons: co-infection with HIV and the development of complex mycobacterial drug resistance patterns [3].

The World Health Organization (WHO) estimates that of the 8.8 million new cases in 2010, ∼3% were caused by multidrug-resistant (MDR) strains of Mycobacterium tuberculosis [4], defined as resistance to at least the two most powerful anti-TB drugs, isoniazid and rifampicin. Furthermore, ∼30,000 cases were thought to be due to extensively drug-resistant (XDR) strains, defined as MDR plus resistance to any fluoroquinolone and at least one second-line injectable anti-TB drug (amikacin, capreomycin or kanamycin). The estimated prevalence of MDR-TB in new and previously treated cases in 2010 was 650,000 worldwide [4].

MDR- and XDR-TB are man-made phenomena that emerge as a result of inadequate treatment of TB and/or poor airborne infection control in healthcare facilities and congregate settings [5]. To resolve the epidemic of MDR-TB, several interventions are needed urgently: rapid case detection, proper infection control, timely access to quality-assured first- and second-line drugs within appropriate regimens, capacity-building to deliver treatment effectively, standardised recording and reporting of treatment outcomes [6] within effective national TB control programmes, and the commitment of national governments [7].

Nine of the countries with the greatest MDR-TB burden worldwide are located in the WHO European Region, …
Effect of Early Palliative Care on Chemotherapy Use and End-of-Life Care in Patients With Metastatic Non–Small-Cell Lung Cancer
Authors: Joseph A. Greer, William F. Pirl, Vicki A. Jackson, Alona Muzikansky, Inga T. Lennes, Rebecca S. Heist, Emily R. Gallagher, Jennifer S. Temel
Journal: Journal of Clinical Oncology (2011)

Prior research shows that introducing palliative care soon after diagnosis for patients with metastatic non-small-cell lung cancer (NSCLC) is associated with improvements in quality of life, mood, and survival. We sought to investigate whether early palliative care also affects the frequency and timing of chemotherapy use and hospice care for these patients.This secondary analysis is based on a randomized controlled trial of 151 patients with newly diagnosed metastatic NSCLC presenting to an outpatient clinic at a tertiary cancer center from June 2006 to July 2009. Participants received either early palliative care integrated with standard oncology care or standard oncology care alone. By 18-month follow-up, 133 participants (88.1%) had died. Outcome measures included: first, number and types of chemotherapy regimens, and second, frequency and timing of chemotherapy administration and hospice referral.The overall number of chemotherapy regimens did not differ significantly by study group. However, compared with those in the standard care group, participants receiving early palliative care had half the odds of receiving chemotherapy within 60 days of death (odds ratio, 0.47; 95% CI, 0.23 to 0.99; P = .05), a longer interval between the last dose of intravenous chemotherapy and death (median, 64.00 days [range, 3 to 406 days] v 40.50 days [range, 6 to 287 days]; P = .02), and higher enrollment in hospice care for longer than 1 week (60.0% [36 of 60 patients] v 33.3% [21 of 63 patients]; P = .004).Although patients with metastatic NSCLC received similar numbers of chemotherapy regimens in the sample, early palliative care optimized the timing of final chemotherapy administration and transition to hospice services, key measures of quality end-of-life care.
Uptake Pathways and Subsequent Intracellular Trafficking in Nonviral Gene Delivery
Authors: Ikramy A Khalil, Kentaro Kogure, Hidetaka Akita, Hideyoshi Harashima
Journal: Pharmacological Reviews (2006)

The successful delivery of therapeutic genes to the designated target cells and their availability at the intracellular site of action are crucial requirements for successful gene therapy. Nonviral gene delivery is currently a subject of increasing attention because of its relative safety and simplicity of use; however, its use is still far from being ideal because of its comparatively low efficiency. Most of the currently available nonviral gene vectors rely on two main components, cationic lipids and cationic polymers, and a variety of functional devices can be added to further optimize the systems. The design of these functional devices depends mainly on our understanding of the mechanisms involved in the cellular uptake and intracellular disposition of the therapeutic genes as well as their carriers. Macromolecules are internalized into cells by a variety of mechanisms, and their intracellular fate is usually linked to the entry mechanism. Therefore, the successful design of a nonviral gene delivery system requires a deep understanding of gene/carrier interactions as well as the mechanisms involved in the interaction of the systems with the target cells. In this article, we review the different uptake pathways that are involved in nonviral gene delivery from a gene delivery point of view. In addition, available knowledge concerning cellular entry and the intracellular trafficking of cationic lipid-DNA complexes (lipoplexes) and cationic polymer-DNA complexes (polyplexes) is summarized.
Brief Report: Association Between Pregnancy Outcomes and Death From Cardiovascular Causes in Parous Women With Systemic Lupus Erythematosus: A Study Using Swedish Population Registries
Authors: May Ching Soh, Catherine Nelson‐Piercy, Fadia Dib, Magnus Westgren, Lesley McCowan, Dharmintra Pasupathy
Journal: Arthritis & Rheumatology (2015)

Objective To determine if maternal placental syndromes (MPS) are associated with an increased risk of death from cardiovascular causes in women with systemic lupus erythematosus (SLE). Methods Between 1973 and 2011, women with SLE and a history of pregnancy were identified using linked Swedish population registries. The outcome was death from primarily cardiovascular causes, defined as death from acute coronary syndrome or coronary artery disease, stroke, or peripheral vascular disease. The exposure was MPS, defined as any hypertensive disorders in pregnancy, stillbirth, placental abruption, or delivery of a small‐for‐gestational‐age infant. The association of preterm delivery (delivery at &lt;34 weeks of gestation) with death from cardiovascular causes was also explored. Risk of death from cardiovascular causes was determined using logistic regression, adjusting for the year of first delivery, duration of SLE, number of inpatient admissions, and cardiovascular risk factors. Results A total of 3,977 women with SLE had 7,410 pregnancies during the study interval. Death from primarily cardiovascular causes occurred in 44 of the 325 women who died (13.5%). The median age at death from cardiovascular causes was 54 years (interquartile range 48–58 years), and these women were more likely to have had hypertension and renal disease. MPS was associated with an increased risk of death from primarily cardiovascular causes (adjusted odds ratio [OR] 2.19 [95% confidence interval (95% CI) 1.14–4.22]), specifically, a history of placental abruption (adjusted OR 5.78 [95% CI 1.61–20.72]). Delivery at &lt;34 weeks of gestation, particularly when combined with MPS, was also associated with an increased risk of death from primarily cardiovascular causes (adjusted OR 2.49 [95% CI 1.06–5.85]). Conclusion MPS in pregnancy is associated with a higher risk of death from primarily cardiovascular causes in women with SLE.
Exercise for depression in elderly residents of care homes: a cluster-randomised controlled trial
Authors: Martin Underwood, Sarah E Lamb, Sandra Eldridge, Bart Sheehan, Anne-Marie Slowther, Anne Spencer, Margaret Thorogood, Nicky Atherton, Stephen A Bremner, Angela Devine, Karla Diaz-Ordaz, David R Ellard, Rachel Potter, Kathleen Spanjers, Stephanie JC Taylor
Journal: The Lancet (2013)
Electrical, contractile and structural remodeling during atrial fibrillation
Authors: M Allessie
Journal: Cardiovascular Research (2002)

The natural history of atrial fibrillation (AF) is characterized by a gradual worsening with time. The recent finding that AF itself produces changes in atrial function and structure has provided a possible explanation for the progressive nature of this arrhythmia. Electrical remodeling (shortening of atrial refractoriness) develops within the first days of AF and contributes to an increase in stability of AF. However, 'domestication of AF' must also depend on a 'second factor' since the persistence of AF continues to increase after electrical remodeling has been completed. Atrial contractile remodeling (loss of contractility) leads to a reduced atrial transport function after cardioversion of AF. An important clinical consequence is that during several days after restoration of sinus rhythm, the risk of atrial thrombus formation is still high. In addition, the reduction of atrial contractility during AF may enhance atrial dilatation which may add to the persistence of AF. Tachycardia-induced structural remodeling takes place in a different time domain (weeks to months). Myolysis probably contributes to the loss of atrial contractile force. Although it might explain the loss of efficacy of pharmacological cardioversion and the development of permanent AF, the role of structural remodeling in the progression of AF is still unclear. Atrial structural remodeling also occurs as a result of heart failure and other underlying cardiovascular diseases. The associated atrial fibrosis might explain intra-atrial conduction disturbances and the susceptibility for AF. Thus, both AF itself and the underlying heart disease are responsible for the development of the arrhythmogenic substrate. New strategies for prevention and termination of AF should be build on our knowledge of the mechanisms and time course of AF-induced atrial remodeling.