89 research outputs found
The Population Genetics of dN/dS
Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. The dN/dS ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. Nevertheless, the dN/dS measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. Here, we study the expected dN/dS ratio for samples drawn from a single population under selection, and we find that in this context, dN/dS is relatively insensitive to the selection coefficient. Moreover, the hallmark signature of positive selection over divergent lineages, dN/dS>1, is violated within a population. For population samples, the relationship between selection and dN/dS does not follow a monotonic function, and so it may be impossible to infer selection pressures from dN/dS. These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples
Thermal Perceptual Thresholds are typical in Autism Spectrum Disorder but Strongly Related to Intra-individual Response Variability
Individuals with autism spectrum disorder (ASD) are often reported to exhibit an apparent indifference to pain or temperature. Leading models suggest that this behavior is the result of elevated perceptual thresholds for thermal stimuli, but data to support these assertions are inconclusive. An alternative proposal suggests that the sensory features of ASD arise from increased intra-individual perceptual variability. In this study, we measured method-of-limits warm and cool detection thresholds in 142 individuals (83 with ASD, 59 with typical development [TD], aged 7–54 years), testing relationships with diagnostic group, demographics, and clinical measures. We also investigated the relationship between detection thresholds and a novel measure of intra-individual (trial-to-trial) threshold variability, a putative index of “perceptual noise.” This investigation found no differences in thermal detection thresholds between individuals with ASD and typical controls, despite large differences between groups in sensory reactivity questionnaires and modest group differences in intra-individual variability. Lower performance IQ, male sex, and higher intra-individual variability in threshold estimates were the most significant predictors of elevated detection thresholds. Although no psychophysical measure was significantly correlated with questionnaire measures of sensory hyporeactivity, large intra-individual variability may partially explain the elevated psychophysical thresholds seen in a subset of the ASD population
understanding and tackling poverty and vulnerability in mountain livelihoods in the hindu kush himalaya
This chapter critically reviews the existing knowledge on livelihoods, poverty, and vulnerability in the Hindu Kush Himalaya (HKH). Development in mountain areas and the practices of people in these areas are uniquely conditioned by distinct characteristics that we term "mountain specificities". Some of these specificities—such as inaccessibility, fragility, and marginality—constrain development. Others—such as abundant biological diversity, ecological niches, and adaptation mechanisms—present development opportunities for mountain people
Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.
BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700
Mechanisms and management of loss of response to anti-TNF therapy for patients with Crohn's disease: 3-year data from the prospective, multicentre PANTS cohort study
This is the final version. Available from Elsevier via the DOI in this record. Background We sought to report the effectiveness of infliximab and adalimumab over the first 3 years of treatment
and to define the factors that predict anti-TNF treatment failure and the strategies that prevent or mitigate loss of
response.
Methods Personalised Anti-TNF therapy in Crohn’s disease (PANTS) is a UK-wide, multicentre, prospective
observational cohort study reporting the rates of effectiveness of infliximab and adalimumab in anti-TNF-naive patients
with active luminal Crohn’s disease aged 6 years and older. At the end of the first year, sites were invited to enrol
participants still receiving study drug into the 2-year PANTS-extension study. We estimated rates of remission across
the whole cohort at the end of years 1, 2, and 3 of the study using a modified survival technique with permutation
testing. Multivariable regression and survival analyses were used to identify factors associated with loss of response
in patients who had initially responded to anti-TNF therapy and with immunogenicity. Loss of response was defined
in patients who initially responded to anti-TNF therapy at the end of induction and who subsequently developed
symptomatic activity that warranted an escalation of steroid, immunomodulatory, or anti-TNF therapy, resectional
surgery, or exit from study due to treatment failure. This study was registered with ClinicalTrials.gov, NCT03088449,
and is now complete.
Findings Between March 19, 2014, and Sept 21, 2017, 389 (41%) of 955 patients treated with infliximab and
209 (32%) of 655 treated with adalimumab in the PANTS study entered the PANTS-extension study (median age
32·5 years [IQR 22·1–46·8], 307 [51%] of 598 were female, and 291 [49%] were male). The estimated proportion of
patients in remission at the end of years 1, 2, and 3 were, for infliximab 40·2% (95% CI 36·7–43·7),
34·4% (29·9–39·0), and 34·7% (29·8–39·5), and for adalimumab 35·9% (95% CI 31·2–40·5), 32·9% (26·8–39·2),
and 28·9% (21·9–36·3), respectively. Optimal drug concentrations at week 14 to predict remission at any later
timepoints were 6·1–10·0 mg/L for infliximab and 10·1–12·0 mg/L for adalimumab. After excluding patients who
had primary non-response, the estimated proportions of patients who had loss of response by years 1, 2, and 3
were, for infliximab 34·4% (95% CI 30·4–38·2), 54·5% (49·4–59·0), and 60·0% (54·1–65·2), and for adalimumab
32·1% (26·7–37·1), 47·2% (40·2–53·4), and 68·4% (50·9–79·7), respectively. In multivariable analysis, loss of
response at year 2 and 3 for patients treated with infliximab and adalimumab was predicted by low anti-TNF drug
concentrations at week 14 (infliximab: hazard ratio [HR] for each ten-fold increase in drug concentration 0·45
[95% CI 0·30–0·67], adalimumab: 0·39 [0·22–0·70]). For patients treated with infliximab, loss of response was
also associated with female sex (vs male sex; HR 1·47 [95% CI 1·11–1·95]), obesity (vs not obese 1·62 [1·08–2·42]),
baseline white cell count (1·06 [1·02–1·11) per 1 × 10⁹ increase in cells per L), and thiopurine dose quartile. Among
patients treated with adalimumab, carriage of the HLA-DQA1*05 risk variant was associated with loss of response
(HR 1·95 [95% CI 1·17–3·25]). By the end of year 3, the estimated proportion of patients who developed anti-drug
antibodies associated with undetectable drug concentrations was 44·0% (95% CI 38·1–49·4) among patients
treated with infliximab and 20·3% (13·8–26·2) among those treated with adalimumab. The development of antidrug antibodies associated with undetectable drug concentrations was significantly associated with treatment
without concomitant immunomodulator use for both groups (HR for immunomodulator use: infliximab 0·40
[95% CI 0·31–0·52], adalimumab 0·42 [95% CI 0·24–0·75]), and with carriage of HLA-DQA1*05 risk variant for
infliximab (HR for carriage of risk variant: infliximab 1·46 [1·13–1·88]) but not for adalimumab (HR 1·60
[0·92–2·77]). Concomitant use of an immunomodulator before or on the day of starting infliximab was associated
with increased time without the development of anti-drug antibodies associated with undetectable drug
concentrations compared with use of infliximab alone (HR 2·87 [95% CI 2·20–3·74]) or introduction of an
immunomodulator after anti-TNF initiation (1·70 [1·11–2·59]). In years 2 and 3, 16 (4%) of 389 patients treated
with infliximab and 11 (5%) of 209 treated with adalimumab had adverse events leading to treatment withdrawal.
Nine (2%) patients treated with infliximab and two (1%) of those treated with adalimumab had serious infections
in years 2 and 3.
Interpretation Only around a third of patients with active luminal Crohn’s disease treated with an anti-TNF drug were
in remission at the end of 3 years of treatment. Low drug concentrations at the end of the induction period predict
loss of response by year 3 of treatment, suggesting higher drug concentrations during the first year of treatment,
particularly during induction, might lead to better long-term outcomes. Anti-drug antibodies associated with
undetectable drug concentrations of infliximab, but not adalimumab, can be predicted by carriage of HLA-DQA1*05
and mitigated by concomitant immunomodulator use for both drugs.Guts UKCrohn’s and Colitis UKCure Crohn’s ColitisAbbVieMerck Sharp and DohmeNapp PharmaceuticalsPfizerCelltrion Healthcar
High temporal resolution monitoring of multiple pollutant responses in drainage from an intensively managed grassland catchment caused by a summer storm
This work presents data on a suite of diffuse pollutants, monitored in a stream
draining an intensively managed grassland on a 30 min time step during a period
of intense rainfall to better understand their sources and pathways. Nitrite (92
mu g l(-1)), particulate phosphorus (107 mu g l(-1)) and soluble phosphorus (74
mu g l(-1)) exceeded environmental limits during base flow. Concentrations of
nitrate and nitrite were decreased during the storm event, whereas all other
pollutants generally increased and exceeded environmental limits where
specified, especially when associated with a small subsidiary hydrograph on the
rising limb of the main hydrograph. Total pollutants loads, when using a 60 min
sampling frequency, would have led to significant over and under-estimations
depending on which 60 min sample set was used. In the worst case, loads of
ammonium could have been under-estimated by 35% or over estimated by 25% with
errors being associated with loads on the rising limb of the hydrograph and more
specifically a small subsidiary hydrograph. This subsidiary hydrograph may have
occurred as a result of runoff from the farm hard standings within the
catchment. Incidental transfer of pollutants associate with this runoff have
masked the overall grassland pollutant response. To better understand these
different source areas and pollutant dynamics, there is a need for novel tracing
techniques to elucidate their relative contribution and pathways
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