bluuebunny/crossref_metadata_2025_split huggingface dataset:
Family history, comorbidity, smoking and other risk factors in microscopic colitis: a case–control study
Authors: Wickbom Anna , Nyhlin Nils , Montgomery Scott M. , Bohr Johan , Tysk Curt 
Published: January 2017

Objectives
Data on heredity, risk factors and comorbidity in microscopic colitis, encompassing collagenous colitis (CC) and lymphocytic colitis (LC), are limited.

Aim
The aim was to carry out a case–control study of family history, childhood circumstances, educational level, marital status, smoking and comorbidity in microscopic colitis.

Methods
A postal questionnaire was sent in 2008–2009 to microscopic colitis patients resident in Sweden and three population-based controls per patient, matched for age, sex and municipality.

Results
Some 212 patients and 627 controls participated in the study. There was an association with a family history of microscopic colitis in both CC [odds ratio (OR): 10.3; 95% confidence interval (CI): 2.1–50.4, P=0.004] and LC (OR not estimated, P=0.008). Current smoking was associated with CC [OR: 4.7; 95% CI: 2.4–9.2, P<0.001) and LC (OR: 3.2; 95% CI: 1.6–6.7, P=0.002). The median age at diagnosis was around 10 years earlier in ever-smokers compared with never-smokers.
CC was associated with a history of ulcerative colitis (UC) (OR: 8.7, 95% CI: 2.2–33.7, P=0.002), thyroid disease (OR: 2.3; 95% CI: 1.1–4.5, P=0.02), coeliac disease (OR: 13.1; 95% CI: 2.7–62.7, P=0.001), rheumatic disease (OR 1.9; 95% CI: 1.0–3.5, P=0.042) and previous appendicectomy (OR: 2.2; 95% CI: 1.3–3.8, P=0.003), and LC with UC (OR: 6.8; 95% CI: 1.7–28.0, P=0.008), thyroid disease (OR: 2.4; 95% CI: 1.1–5.4, P=0.037) and coeliac disease (OR: 8.7; 95% CI: 2.8–26.7, P<0.001).

Conclusion
Association with a family history of microscopic colitis indicates that familial factors may be important. The association with a history of UC should be studied further as it may present new insights into the pathogenesis of microscopic colitis and UC.
Quality of Life and Parental Worrying in a National Cohort of Biliary Atresia Children Living With Their Native Livers
Authors: Lampela Hanna , Pakarinen Mikko P. , Jahnukainen Timo , Jalanko Hannu , Kosola Silja 
Published: January 2017

ABSTRACTObjectives:The aim of the study was to evaluate health‐related quality of life (HRQoL) and parental distress in a national cohort of children with biliary atresia (BA) with their native livers in relation to BA complications and HRQoL of normal population controls.Methods:We invited all Finnish children with BA surviving with their native livers at age 2 to 18 years to participate in 2009 and in 2014. Parents filled the Pediatric Quality of Life Inventory (PedsQL) proxy questionnaire, a survey of their child's health and evaluated parental distress on a visual‐analog scale from 0 to 7. Overall participation rates were 80% (12/15) for the longitudinal and 83% (20/24) for the cross‐sectional assessment. A control population of 324 children matched for age and sex was randomly picked, and 108 (33%) participated.Results:Overall, patients and controls had comparable HRQoL. Patients reported significantly lower scores for school functioning (P = 0.004) as depicted by missing school or day care due to hospital visits. Eighty‐five percent of parents reported extreme worry (7.0) when hearing their child's BA diagnosis. At 6 years after diagnosis, parents reported significantly less worry: median score 3.8 (interquartile range 3.0–5.4, P < 0.001 for difference). Parents of patients with optimal health were less worried than parents whose children's health was suboptimal: median worry score 3.3 (3.0–4.8) versus 5.3 (3.8–5.9), P = 0.05.Conclusions:BA patients’ HRQoL was comparable to matched peers in general but reduced by missing school days due to frequent hospital visits. At diagnosis, parents experienced considerable worry that diminished over the years after successful portoenterostomy, especially if the child's health was optimal.
Acquired TEF in Hodgkin Lymphoma in a Child: A Rare Clinical Association
Authors: Munikoty Vinay , Bhatia Anmol , Bansal Deepak , Das Ashim , Khandelwal Niranjan 
Published: January 2017

Background:
Malignancy is the most common etiology of acquired fistulae between the tracheobronchial tree and esophagus. The majority are due to either primary bronchial or esophageal carcinoma, and are typically observed in adult population. The occurrence of tracheoesophageal fistula (TEF) in patients with Hodgkin lymphoma is a rare phenomenon.

Observation:
We report a rare case of Hodgkin lymphoma with TEF in a 10-year-old girl at presentation. She also developed pulmonary tuberculosis later during the follow up. She was fed through a nasogastric tube to avoid aspiration through the fistulous tract. She did well with chemotherapy and anti-tubercular therapy.

Conclusions:
Our case suggests TEF in Hodgkin lymphoma at the time of diagnosis is a rare complication in pediatric age group. Lymphoma-related TEF require far less active intervention, as against esophageal or bronchial malignancy related TEF.
Whole-Body MRI Virtual Autopsy Using Diffusion-weighted Imaging With Background Suppression (DWIBS) at 3 T in a Child Succumbing to Chordoma
Authors: Andronikou Savvas , Kemp Marnie L. , Meiring Michelle 
Published: January 2017

Background:
We report the use of diffusion-weighted imaging with background suppression (DWIBS) in pediatric virtual magnetic resonance imaging (MRI) autopsy of a child who succumbed to chordoma.

Case Description:
A 10-year-old girl who succumbed to relapse of a chordoma underwent whole-body virtual MRI autopsy 12 hours postmortem with short Tau inversion recovery (STIR) and DWIBS on 3 T, which demonstrated the primary mass, local and cardiac invasion, and metastatic disease to the thorax, abdomen, head/neck, and musculoskeletal system.

Conclusions:
Postmortem virtual MRI autopsy including DWIBS successfully demonstrated the transthoracic spread of chordoma and invasion of the heart, resulting in blood-borne metastases. Motion and respiratory artifact were not factors during virtual autopsy using DWIBS on 3 T, making ideal use of this technology.
Mobility and Clinic Switching Among Postpartum Women Considered Lost to HIV Care in South Africa
Authors: Clouse Kate , Vermund Sten H. , Maskew Mhairi , Lurie Mark N. , MacLeod William , Malete Given , Carmona Sergio , Sherman Gayle , Fox Matthew P. 
Published: January 2017

Objective:
Retention in HIV care, particularly among postpartum women, is a challenge to national antiretroviral therapy programs. Retention estimates may be underestimated because of unreported transfers. We explored mobility and clinic switching among patients considered lost to follow-up (LTFU).

Design:
Observational cohort study.

Methods:
Of 788 women initiating antiretroviral therapy during pregnancy at 6 public clinics in Johannesburg, South Africa, 300 (38.1%) were LTFU (no visit ≥3 months). We manually searched for these women in the South African National Health Laboratory Services database to assess continuity of HIV care. We used geographic information system tools to map mobility to new facilities.

Results:
Over one-third (37.6%) of women showed evidence of continued HIV care after LTFU. Of these, 67.0% continued care in the same province as the origin clinic. Compared with those who traveled outside of the province for care, these same-province “clinic shoppers” stayed out-of-care longer {median 373 days [interquartile range (IQR): 175–790] vs. 175.5 days (IQR: 74–371)} and had a lower CD4+ cell count on re-entry [median 327 cells/μL (IQR: 196–576) vs. 493 cells/μL (IQR: 213–557). When considering all women with additional evidence of care as engaged in care, cohort LTFU dropped from 38.1% to 25.0%.

Conclusions:
We found evidence of continued care after LTFU and identified local and national clinic mobility among postpartum women. Laboratory records do not show all clinic visits and manual matching may have been under- or overestimated. A national health database linked to a unique identifier is necessary to improve reporting and patient care among highly mobile populations.
Perforator Phase Contrast Angiography of Deep Inferior Epigastric Perforators
Authors: Yang Xiangyu , Miller Michael J. , Friel Harry T. , Slijepcevic Allison , Knopp Michael V. 
Published: January 2017

Objective
The aim of this study was to demonstrate the feasibility of in vivo perforator visualization by a newly proposed magnetic resonance–based perforator phase contrast angiography (pPCA) technique for deep inferior epigastric perforator (DIEP) flap surgery and to prospectively compare its image quality and clinical value with computed tomographic angiography (CTA), the state-of-the-art perforator imaging technique.

Materials and Methods
Institutional review board approval and informed consent were obtained. DIEP pPCA and CTA data were acquired in 10 female patients before DIEP flap surgery. Image findings were compared between the two techniques and with literature reports.

Results
The overall image quality is negatively correlated with patient BMI for CTA, but positively correlated with BMI for pPCA. Compared with CTA, pPCA has significantly better image quality (P = 0.005), signal-to-noise ratio (P < 0.001), and contrast-to-noise ratio (perforator-to-muscle, P < 0.001; perforator-to-fat, P = 0.014). It also has preferable clinical value ratings, although not statistically significant (P = 0.388). There is a good agreement (84%) between perforators detected by pPCA and CTA. Perforator location deviations between pPCA and CTA are compatible with the precision required for plastic surgery. Perforator size measured by pPCA seems to be more accurate than CTA, as it is 0.8 ± 0.3 mm smaller (P < 0.001), consistent with the reported 0.5 to 1.2 mm overestimation by CTA. There is no significant difference in perforator intramuscular course assessment (P = 0.415).

Conclusions
The developed magnetic resonance–based pPCA technique presents superior image quality, better vessel contrast, and more accurate perforator anatomy than the x-ray–based CTA. pPCA has the potential to emerge as the preferred preoperative planning tool for perforator flap reconstructive surgery.
Semaphorin-Plexin signaling influences early ventral telencephalic development and thalamocortical axon guidance
Authors: Mitsogiannis Manuela D. , Little Graham E. , Mitchell Kevin J. 
Published: January 2017

AbstractBackgroundSensory processing relies on projections from the thalamus to the neocortex being established during development. Information from different sensory modalities reaching the thalamus is segregated into specialized nuclei, whose neurons then send inputs to cognate cortical areas through topographically defined axonal connections.Developing thalamocortical axons (TCAs) normally approach the cortex by extending through the subpallium; here, axonal navigation is aided by distributed guidance cues and discrete cell populations, such as the corridor neurons and the internal capsule (IC) guidepost cells. In mice lacking Semaphorin-6A, axons from the dorsal lateral geniculate nucleus (dLGN) bypass the IC and extend aberrantly in the ventral subpallium. The functions normally mediated by Semaphorin-6A in this system remain unknown, but might depend on interactions with Plexin-A2 and Plexin-A4, which have been implicated in other neurodevelopmental processes.MethodsWe performed immunohistochemical and neuroanatomical analyses of thalamocortical wiring and subpallial development inSema6aandPlxna2;Plxna4null mutant mice and analyzed the expression of these genes in relevant structures.ResultsInPlxna2;Plxna4double mutants we discovered TCA pathfinding defects that mirrored those observed inSema6amutants, suggesting that Semaphorin-6A–Plexin-A2/Plexin-A4 signaling might mediate dLGN axon guidance at subpallial level.In order to understand where and when Semaphorin-6A, Plexin-A2 and Plexin-A4 may be required for proper subpallial TCA guidance, we then characterized their spatiotemporal expression dynamics during early TCA development. We observed that the thalamic neurons whose axons are misrouted in these mutants normally express Semaphorin-6A but not Plexin-A2 or Plexin-A4. By contrast, all three proteins are expressed in corridor cells and other structures in the developing basal ganglia.This could be consistent with the Plexins acting as guidance signals through Sema6A as a receptor on dLGN axons, and/or with an indirect effect on TCA guidance due to functions in morphogenesis of subpallial intermediate targets. In support of the latter possibility, we observed that in bothPlxna2;Plxna4andSema6amutants some IC guidepost cells abnormally localize in correspondence of the ventral path misrouted TCAs elongate into.ConclusionsThese findings implicate Semaphorin-6A–Plexin-A2/Plexin-A4 interactions in dLGN axon guidance and in the spatiotemporal organization of guidepost cell populations in the mammalian subpallium.
Metacognitive impairments extend perceptual decision making weaknesses in compulsivity
Authors: Hauser Tobias U. , Allen Micah ,   NSPN Consortium, Rees Geraint , Dolan Raymond J. 
Published: January 2017

AbstractAwareness of one’s own abilities is of paramount importance in adaptive decision making. Psychotherapeutic theories assume such metacognitive insight is impaired in compulsivity, though this is supported by scant empirical evidence. In this study, we investigate metacognitive abilities in compulsive participants using computational models, where these enable a segregation between metacognitive and perceptual decision making impairments. We examined twenty low-compulsive and twenty high-compulsive participants, recruited from a large population-based sample, and matched for other psychiatric and cognitive dimensions. Hierarchical computational modelling of the participants’ metacognitive abilities on a visual global motion detection paradigm revealed that high-compulsive participants had a reduced metacognitive ability. This impairment was accompanied by a perceptual decision making deficit whereby motion-related evidence was accumulated more slowly in high compulsive participants. Our study shows that the compulsivity spectrum is associated with a reduced ability to monitor one’s own performance, over and above any perceptual decision making difficulty.
A Two-Process Model for Circadian and Sleep-dependent Modulation of Pain Sensitivity
Authors: Toporikova Natalia , Hagenauer Megan Hastings , Ferguson Paige , Booth Victoria 
Published: January 2017

AbstractPain sensitivity is strongly modulated by time of day and by prior sleep behavior. These two factors, governed by the circadian rhythm and homeostatic sleep drive, respectively, likewise dictate the timing and duration of sleep. The fields of sleep and circadian research have identified much of the physiology underlying the circadian rhythm and homeostatic sleep drive with mathematical modeling playing an important role in understanding how these two processes interact to affect sleep behavior. We hypothesize that the daily rhythm of pain sensitivity and its sleep-dependent modulation reflect an interaction of the circadian rhythm and homeostatic sleep drive. To investigate this hypothesis, we adapt the formalism of a classic mathematical model for the regulation of sleep behavior by the circadian rhythm and homeostatic sleep drive, called the Two Process model, to simulate the interaction of these two processes on pain sensitivity. To construct the model, we utilize data from experimental reports on the daily rhythmicity of pain sensitivity in humans to define a “daily pain sensitivity” function. We decompose this function into two processes: a sleep-dependent processS(t) that follows the homeostatic sleep drive and a circadian processC(t) that is dictated by the circadian rhythm. By simulating different sleep schedules with the original Two Process model, we compute changes in the sleep-dependent processS(t) that modulates pain sensitivity. By combiningS(t) with the circadian processC(t), our model predicts resultant changes in the daily pain sensitivity rhythm. We illustrate model predictions for changes in pain sensitivity due to sleep deprivation, sleep restriction and shift work schedules. We believe that this model may be a useful tool for pain management by providing predictions of the variations in pain sensitivity due to changing sleep schedules.
Invisible noise obscures visible signal in insect motion detection
Authors: Tarawneh Ghaith , Nityananda Vivek , Rosner Ronny , Errington Steven , Herbert William , Cumming Bruce G. , Read Jenny C. A. , Serrano-Pedraza Ignacio 
Published: January 2017

1AbstractThe motion energy model is the standard account of motion detection in animals from beetles to humans. Despite this common basis, we show here that a difference in the early stages of visual processing between mammals and insects leads this model to make radically different behavioural predictions. In insects, early filtering is spatially lowpass, which makes the surprising prediction that motion detection can be impaired by “invisible” noise, i.e. noise at a spatial frequency that elicits no response when presented on its own as a signal. We confirm this prediction using the optomotor response of praying mantisSphodromantis lineola. This does not occur in mammals, where spatially bandpass early filtering means that linear systems techniques, such as deriving channel sensitivity from masking functions, remain approximately valid. Counter-intuitive effects such as masking by invisible noise may occur in neural circuits wherever a nonlinearity is followed by a difference operation.
Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification
Authors: Robertson Fiona M. , Gundappa Manu Kumar , Grammes Fabian , Hvidsten Torgeir R. , Redmond Anthony K. , Lien Sigbjørn , Martin Samuel A.M. , Holland Peter W. H. , Sandve Simen R. , Macqueen Daniel J. 
Published: January 2017

AbstractThe functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification is often highly temporally-detached from WGD. Salmonid fish, whose ancestor experienced WGD by autotetraploidization ~95 Ma (i.e. ‘Ss4R’), fit such a ‘time-lag’ model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model called ‘Lineage-specific Ohnologue Resolution’ (LORe) to address the phylogenetic and functional consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One quarter of each salmonid genome, harbouring at least 4,500 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions > 50 Myr post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that promoted salmonid species radiation. We show that LORe ohnologues are enriched for different functions than ‘older’ ohnologues that began diverging in the salmonid ancestor. LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear ‘explosively’, but can arise gradually over tens of Myr, promoting lineage-specific diversification regimes under prevailing ecological pressures.
A note on noise suppression in cell-size control
Authors: Singh Abhyudai 
Published: January 2017

AbstractDiverse cell types employ mechanisms to maintain size homeostasis and minimize aberrant fluctuations in cell size. It is well known that exponential cellular growth can drive unbounded intercellular variations in cell size, if the timing of cell division is size independent. Hence coupling of division timing to size is an essential feature of size control. We formulate a stochastic model, where exponential cellular growth is coupled with random cell division events, and the rate at which division events occur increases as a power function of cell size. Interestingly, in spite of nonlinearities in the stochastic dynamical model, statistical moments of the newborn cell size can be determined in closed form, providing fundamental limits to suppression of size fluctuations. In particular, formulas reveal that the magnitude of fluctuations in the newborn size is determined by the inverse of the size exponent in the division rate, and this relationship is independent of other model parameters, such as the growth rate. We further expand these results to consider randomness in the partitioning of mother cell size among daughters at the time of division. The sensitivity of newborn size fluctuations to partitioning noise is found to monotonically decrease, and approach a non-zero value, with increasing size exponent in the division rate. Finally, we discuss how our analytical results provide limits on noise control in commonly used models for cell size regulation.
Decoding sequence-level information to predict membrane protein expression
Authors: Saladi Shyam M. , Javed Nauman , Müller Axel , Clemons William M. 
Published: January 2017

SummaryThe expression of integral membrane proteins (IMPs) remains a major bottleneck in the characterization of this important protein class. IMP expression levels are currently unpredictable, which renders the pursuit of IMPs for structural and biophysical characterization challenging and inefficient. Experimental evidence demonstrates that changes within the nucleotide or amino-acid sequence for a given IMP can dramatically affect expression; yet these observations have not resulted in generalizable approaches to improved expression. Here, we develop a data-driven statistical predictor named IMProve, that, using only sequence information, increases the likelihood of selecting an IMP that expresses inE. coli.The IMProve model, trained on experimental data, combines a set of sequence-derived features resulting in an IMProve score, where higher values have a higher probability of success. The model is rigorously validated against a variety of independent datasets that contain a wide range of experimental outcomes from various IMP expression trials. The results demonstrate that use of the model can more than double the number of successfully expressed targets at any experimental scale. IMProve can immediately be used to identify favorable targets for characterization.