Atomistic dynamics of sulfur-deficient high-symmetry grain boundaries in molybdenum disulfide.
As a common type of structural defect, grain boundaries (GBs) play an important role in tailoring the physical and chemical properties of bulk crystals and their two-dimensional (2D) counterparts such as graphene and molybdenum disulfide (MoS2). In this study, we explore the atomic structures and dynamics of three kinds of high-symmetry GBs (α, β and γ) in monolayer MoS2. Atomic-resolution transmission electron microscopy (TEM) is used to characterize their formation and evolutionary dynamics, and atomistic simulation based analysis explains the size distribution of α-type GBs observed under TEM and the inter-GB interaction, revealing the stabilization mechanism of GBs by pre-existing sulfur vacancies. The results elucidate the correlation between the observed GB dynamics and the migration of sulfur atoms across GBs via a vacancy-mediated mechanism, offering a new perspective for GB engineering in monolayer MoS2, which may be generalized to other transition metal dichalcogenides.


Findings of the first consensus conference on medical emergency teams.
Studies have established that physiologic instability and services mismatching precede adverse events in hospitalized patients. In response to these considerations, the concept of a Rapid Response System (RRS) has emerged. The responding team is commonly known as a medical emergency team (MET), rapid response team (RRT), or critical care outreach (CCO). Studies show that an RRS may improve outcome, but questions remain regarding the benefit, design elements, and advisability of implementing a MET system. In June 2005 an International Conference on Medical Emergency Teams (ICMET) included experts in patient safety, hospital medicine, critical care medicine, and METs. Seven of 25 had no experience with an RRS, and the remainder had experience with one of the three major forms of RRS. After preconference telephone and e-mail conversations by the panelists in which questions to be discussed were characterized, literature reviewed, and preliminary answers created, the panelists convened for 2 days to create a consensus document. Four major content areas were addressed: What is a MET response? Is there a MET syndrome? What are barriers to METS? How should outcome be measured? Panelists considered whether all hospitals should implement an RRS. Patients needing an RRS intervention are suddenly critically ill and have a mismatch of resources to needs. Hospitals should implement an RRS, which consists of four elements: an afferent, "crisis detection" and "response triggering" mechanism; an efferent, predetermined rapid response team; a governance/administrative structure to supply and organize resources; and a mechanism to evaluate crisis antecedents and promote hospital process improvement to prevent future events.


Clinical and angiographic findings of complete atrioventricular block in acute inferior myocardial infarction.
The angiographic findings and prognosis of patients with complete atrioventricular block (AVB) complicating acute inferior myocardial infarction (MI) remain unclear. The clinical and angiographic findings of 70 consecutive patients with complete AVB were compared with those of 319 patients with inferior MI without AVB (control group) admitted within the same study period. Patients with complete AVB were older (68 +/- 12 vs 63 +/- 13 years; P = 0.004) and clustered with clinical features indicative of larger infarct size, such as right ventricular infarction, cardiogenic shock, or low left ventricular ejection fraction (LVEF). The onset of the complete AVB was observed within 24 hours in 62 (88.6%), preceded by second-degree AVB in 26 (37.1%) and the escape QRS complex was wide in 8 (11.4%) patients. In patients with complete AVB, a dominant right coronary artery occlusion was found in >95% of cases and in-hospital mortality was increased (27.1% vs 10.7%; P = 0.000), especially in those with widen QRS escape rhythm (75.0%). Reperfusion therapy had a positive impact on the natural course of complete AVB. Complete AVB in acute inferior MI was associated with advanced age and larger infarct size. Complete AVB was virtually always caused by dominant right coronary artery occlusion. The in-hospital mortality was significantly higher, but improved by reperfusion therapy. No permanent pacemaker is performed at a mean follow-up of 47 months.


Timing of surgery in thoracolumbar trauma: is early intervention safe?
The understanding of the optimal surgical timing for stabilization in thoracolumbar fractures is severely limited. Thoracolumbar spine fractures can be devastating injuries and are often associated with significant morbidity and mortality. The role of early surgical stabilization (within 48-72 hours of injury) as a vehicle to improve outcomes in these patients has generated significant interest. Goals of early stabilization include improved neurological recovery, faster pulmonary recovery, improved pain control, and decreased health care costs. Opponents cite the potential for increased bleeding, hypotension, and the risk of further cord injury as a few factors that weigh against early stabilization. The concept of spinal cord injury and its relationship to surgical timing remains in question. However, when neurological outcomes are eliminated from the equation, certain measures have shown positive influences from prompt surgical fixation. Early fixation of thoracolumbar spine fractures can significantly decrease the duration of hospital stay and the number of days in the intensive care unit. Additionally, prompt stabilization can reduce rates of pulmonary complications. This includes decreased rates of pneumonia and fewer days on ventilator support. Cost analysis revealed as much as $80,000 in savings per patient with early stabilization. All of these benefits come without an increase in morbidity or evidence of increased mortality. In addition, there is no evidence that early stabilization has any ill effect on the injured or uninjured spinal cord. Based on the existing data, early fixation of thoracolumbar fractures has been linked with positive outcomes without clear evidence of negative impacts on the patient's neurological status, associated morbidities, or mortality. These procedures can be viewed as "damage control" and may consist of simple posterior instrumentation or open reductions with internal fixation as indicated. Based on the current literature it is advisable to proceed with early surgical stabilization of thoracolumbar fractures in a well-resuscitated patient, unless extenuating medical conditions would prevent it.


Excitatory GABAergic signalling is associated with benzodiazepine resistance in status epilepticus.
Status epilepticus is defined as a state of unrelenting seizure activity. Generalized convulsive status epilepticus is associated with a rapidly rising mortality rate, and thus constitutes a medical emergency. Benzodiazepines, which act as positive modulators of chloride (Cl-) permeable GABAA receptors, are indicated as first-line treatment, but this is ineffective in many cases. We found that 48% of children presenting with status epilepticus were unresponsive to benzodiazepine treatment, and critically, that the duration of status epilepticus at the time of treatment is an important predictor of non-responsiveness. We therefore investigated the cellular mechanisms that underlie acquired benzodiazepine resistance, using rodent organotypic and acute brain slices. Removing Mg2+ ions leads to an evolving pattern of epileptiform activity, and eventually to a persistent state of repetitive discharges that strongly resembles clinical EEG recordings of status epilepticus. We found that diazepam loses its antiseizure efficacy and conversely exacerbates epileptiform activity during this stage of status epilepticus-like activity. Interestingly, a low concentration of the barbiturate phenobarbital had a similar exacerbating effect on status epilepticus-like activity, while a high concentration of phenobarbital was effective at reducing or preventing epileptiform discharges. We then show that the persistent status epilepticus-like activity is associated with a reduction in GABAA receptor conductance and Cl- extrusion capability. We explored the effect on intraneuronal Cl- using both gramicidin, perforated-patch clamp recordings and Cl- imaging. This showed that during status epilepticus-like activity, reduced Cl- extrusion capacity was further exacerbated by activity-dependent Cl- loading, resulting in a persistently high intraneuronal Cl-. Consistent with these results, we found that optogenetic stimulation of GABAergic interneurons in the status epilepticus-like state, actually enhanced epileptiform activity in a GABAAR dependent manner. Together our findings describe a novel potential mechanism underlying benzodiazepine-resistant status epilepticus, with relevance to how this life-threatening condition should be managed in the clinic.


Restorative regeneration of digital tips in the African clawed frog (Xenopus laevis daudin).
Localized, specialized structures are carried on the tips of digits of many amniote and certain non-amniote tetrapods. The pes of some members of Pipidae represents a rare example among tetrapods of differential expression of digital tip form (clawed vs. non-clawed digits). As a step towards understanding how such localized forms are generated and maintained, we conducted a series of amputation experiments and observed, through the process of regeneration, the potential for reconstitution, at the tissue and organ level, of the different digit tip morphologies. Results of this study reveal that immediately following metamorphosis specialized digit tip structures are regenerated with a high degree of structural and spatial accuracy by a process that essentially replicates normal development in recently metamorphosed Xenopus laevis froglets. Furthermore, this regenerative capacity is maintained in juveniles 4 months beyond metamorphosis, and also in adults of 1 year or more in age, indicating that metamorphosis-specific conditions do not exclusively facilitate regeneration of digit tips. In addition, regenerative capacity is maintained through repeated bouts of amputation and regeneration, indicating deep-seated digit identity and retention of the distinct digit tip developmental programs within the digits. Together, these data suggest that the developmental programing responsible for the formation of the discrete digital tip morphologies is located regionally within each digit, and that it is retained through time. Our results suggest that Xenopus can serve as a model organism for exploring the molecular underpinnings of digit tip formation because regeneration leads to morphologically identical structures to those of the original digit tips.


Stress-related psychopathology during the COVID-19 pandemic.
The COVID-19 pandemic has introduced widespread societal changes that have required ongoing adaptation. Unsurprisingly, stress-related psychopathology has increased during the pandemic, in both children and adults. We review these patterns through the lens of several leading conceptual models of the link between stress and psychopathology. Some of these models focus on characteristics of environmental stressors-including cumulative risk, specific stressor types, and stress sensitization approaches. Understanding the specific aspects of environmental stressors that are most likely to lead to psychopathology can shed light on who may be in most need of clinical intervention. Other models center on factors that can buffer against the onset of psychopathology following stress and the mechanisms through which stressors contribute to emergent psychopathology. These models highlight specific psychosocial processes that may be most usefully targeted by interventions to reduce stress-related psychopathology. We review evidence for each of these stress models in the context of other widescale community-level disruptions, like natural disasters and terrorist attacks, alongside emerging evidence for these stress pathways from the COVID-19 pandemic. We discuss clinical implications for developing interventions to reduce stress-related psychopathology during the pandemic, with a focus on brief, digital interventions that may be more accessible than traditional clinical services.


Microfluidics: Emerging prospects for anti-cancer drug screening.
Cancer constitutes a heterogenic cellular system with a high level of spatio-temporal complexity. Recent discoveries by systems biologists have provided emerging evidence that cellular responses to anti-cancer modalities are stochastic in nature. To uncover the intricacies of cell-to-cell variability and its relevance to cancer therapy, new analytical screening technologies are needed. The last decade has brought forth spectacular innovations in the field of cytometry and single cell cytomics, opening new avenues for systems oncology and high-throughput real-time drug screening routines. The up-and-coming microfluidic Lab-on-a-Chip (LOC) technology and micro-total analysis systems (μTAS) are arguably the most promising platforms to address the inherent complexity of cellular systems with massive experimental parallelization and 4D analysis on a single cell level. The vast miniaturization of LOC systems and multiplexing enables innovative strategies to reduce drug screening expenditures while increasing throughput and content of information from a given sample. Small cell numbers and operational reagent volumes are sufficient for microfluidic analyzers and, as such, they enable next generation high-throughput and high-content screening of anti-cancer drugs on patient-derived specimens. Herein we highlight the selected advancements in this emerging field of bioengineering, and provide a snapshot of developments with relevance to anti-cancer drug screening routines.


From statistical associations to causation: what developmentalists can learn from instrumental variables techniques coupled with experimental data.
In this article, the authors aim to make accessible the careful application of a method called instrumental variables (IV). Under the right analytic conditions, IV is one promising strategy for answering questions about the causal nature of associations and, in so doing, can advance developmental theory. The authors build on prior work combining the analytic approach of IV with the strengths of random assignment design, whether the experiment is conducted in the lab setting or in the "real world." The approach is detailed through an empirical example about the effects of maternal education on children's cognitive and school outcomes. With IV techniques, the authors address whether maternal education is causally related to children's cognitive development or whether the observed associations reflect some other characteristic related to parenting, income, or personality. The IV estimates show that maternal education has a positive effect on the cognitive test scores of children entering school. The authors conclude by discussing opportunities for applying these same techniques to address other questions of critical relevance to developmental science.


Atlas-based rib-bone detection in chest X-rays.
This paper investigates using rib-bone atlases for automatic detection of rib-bones in chest X-rays (CXRs). We built a system that takes patient X-ray and model atlases as input and automatically computes the posterior rib borders with high accuracy and efficiency. In addition to conventional atlas, we propose two alternative atlases: (i) automatically computed rib bone models using Computed Tomography (CT) scans, and (ii) dual energy CXRs. We test the proposed approach with each model on 25 CXRs from the Japanese Society of Radiological Technology (JSRT) dataset and another 25 CXRs from the National Library of Medicine CXR dataset. We achieve an area under the ROC curve (AUC) of about 95% for Montgomery and 91% for JSRT datasets. Using the optimal operating point of the ROC curve, we achieve a segmentation accuracy of 88.91±1.8% for Montgomery and 85.48±3.3% for JSRT datasets. Our method produces comparable results with the state-of-the-art algorithms. The performance of our method is also excellent on challenging X-rays as it successfully addressed the rib-shape variance between patients and number of visible rib-bones due to patient respiration.


Comparison of the incidence and predicted risk of early surgical site infections after breast reduction.
In plastic surgery, clean, elective operations such as breast reductions are anticipated to have low risk factors for infections (1.1-2.1%). To further lower or prevent surgical site infections (SSI), the efficacy of a prophylactic administration of anti-microbacterials remains a current controversial issue in plastic surgery. We report here the findings of a retrospective study in which we examined two groups of patients with breast reductions, one of which received a single-shot antimicrobacterial prophylaxis with cefuroxime preoperatively and the other who were given no anti-microbacterials. The aims were to determine the early SSI incidence of both groups, to classify breast reductions with respect to their inherent SSI risk by two widespread, combined risk scores, i.e., the National Nosocomial Infection Surveillance (NNIS) score and the Study on the Efficacy of Nosocomial Infection Control (SENIC) score, and to compare the actual SSI incidence to the predicted risk of the scores. In the divisions of plastic surgery at two hospitals, 153 patients (group I) and 136 patients (group II) could be included in the study in the 4-year period April 1997 to December 2001. Excluded were all patients with unilateral breast reduction or breast reconstruction and patients who were followed up less than 30 days postoperatively. The two groups were comparable with respect to demographic and clinical features such as age and risk factors, and there were no detectable significant intergroup differences in the general perioperative data. According to the NNIS and the SENIC scores, all operations were "clean," and the American Society of Anesthesiologists (ASA) score was < 3 in all patients. Although the mean duration of the operation was significantly different in the two groups (190 min in group I, 160 min in group II; p < 0.001, Mann-Whitney test; 75th percentile at and 4 and 3 h, respectively), it was longer than 2 h in both groups. The incidence of early infections was 3.9% in the first group, compared with 3.6% in the second group (p = 1.0, odds ratio = 1.07, 95% CI = 0.32-3.6). All infections were local and superficial; no general symptoms were noticed. Three patients had to be readmitted and two of these were reoperated. The rate of infections for both groups was higher than generally anticipated for this kind of clean operations and higher than predicted by the NNIS score for medium risk (predicted risk of 2.9%). The reason for this discrepancy is that the NNIS score is an inpatient risk score which does not include a postdischarge SSI surveillance. Using the NNIS definition of SSI we would have had an infection rate of 0% in both groups in our study. According to the SENIC score, breast reductions can be classified also as medium risk of SSI with a predicted risk of 3.9%, which showed a nearly perfect correspondence with the actual SSI incidence in both study groups. The reason for this increased, medium risk is the factor "operation time > 2 h," which is obviously an inherent risk factor in breast reductions. Among the multitude of patient and nonpatient SSI risk factors, in healthy women operation time was the only factor which could be clearly identified.


An approximate maximum likelihood approach, applied to phylogenetic trees.
A novel type of approximation scheme to the maximum likelihood (ML) approach is presented and discussed in the context of phylogenetic tree reconstruction from aligned DNA sequences. It is based on a parameterized approximation to the conditional distribution of hidden variables (related, e.g., to the sequences of unobserved branch point ancestors) given the observed data. A modified likelihood, based on the extended data, is then maximized with respect to the parameters of the model as well as to those involved in the approximation. With a suitable form of the approximation, the proposed method allows for simpler updating of the parameters, at the cost of an increased parameter count and a slight decrease in performance. The method is tested on phylogenetic tree reconstruction from artificially generated sequences, and its performance is compared to that of ML, showing that the approach is competitive for reasonably similar sequences. The method is also applied to real DNA sequences from primates, yielding a result consistent with those obtained by other standard algorithms.


A psychometric appraisal of the dundee ready education environment measure in a medical school in Chile.
The Dundee Ready Education Environment Measure (DREEM) is used in the curricular development of future health professionals worldwide, but often without first locally testing its psychometric qualities, for example, construct validity and internal consistency. These characteristics are modified by different environments, but must be locally appropriate to obtain unequivocal and reliable conclusions about the strong and weak areas of a curriculum. Here, we report the results of the psychometric testing of DREEM results in our institution in Chile. All 1st-5th-year undergraduate medical students were asked to respond the DREEM questionnaire. The construct validity of the results was assessed by an exploratory factor analysis (EFA), and their internal consistency was assessed by Cronbach's α. The Institutional Review Board approved the study, and each student signed an informed consent. A total of 304 (88%) eligible students, aged 22 ± 2 years, 46% of females, answered the questionnaire. The EFA determined four instead of the original DREEM's five subareas with clearly different item contents. The inner consistencies of the locally defined subareas of teaching, learning, teachers and organizational aspects, and self-perception surpassed the originals with Cronbach's α values of 0.79, 0.78, 0.77, and 0.82, respectively. The optimal psychometric structure to accurately interpret our DREEM results differed from both the original and previous similar studies, including one from Chile. There are several potential explanations for these differences, but most importantly, they underline the need to first define the psychometric characteristics of the test results, to obtain accurate conclusions about the strengths and the weaknesses of a curriculum.


Interactions between THC and cannabidiol in mouse models of cannabinoid activity.
Interest persists in characterizing potential interactions between Delta(9)-tetrahydocannabinol (THC) and other marijuana constituents such as cannabidiol (CBD). Such interactions may have important implications for understanding the long-term health consequences of chronic marijuana use as well as for attempts to develop therapeutic uses for THC and other CB(1) agonists. We investigated whether CBD may modulate the pharmacological effects of intravenously administered THC or inhaled marijuana smoke on hypoactivity, antinociception, catalepsy, and hypothermia, the well characterized models of cannabinoid activity. Intravenously administered CBD possessed very little activity on its own and, at a dose equal to a maximally effective dose of THC (3 mg/kg), failed to alter THC's effects on any measure. However, higher doses of CBD (ED(50)=7.4 mg/kg) dose-dependently potentiated the antinociceptive effects of a low dose of THC (0.3 mg/kg). Pretreatment with 30 mg/kg CBD, but not 3 mg/kg, significantly elevated THC blood and brain levels. No interactions between THC and CBD were observed in several variations of a marijuana smoke exposure model. Either quantities of CBD were applied directly to marijuana, CBD and THC were both applied to placebo plant material, or mice were pretreated intravenously with 30 mg/kg CBD before being exposed to marijuana smoke. As the amount of CBD found in most marijuana strains in the US is considerably less than that of THC, these results suggest that CBD concentrations relevant to what is normally found in marijuana exert very little, if any, modulatory effects on CB(1)-receptor-mediated pharmacological effects of marijuana smoke.


Systemic morphine suppresses noxious stimulus-evoked Fos protein-like immunoreactivity in the rat spinal cord.
Previous experiments have shown that noxious stimulation increases expression of the c-fos proto-oncogene in subpopulations of spinal cord neurons. c-fos expression was assessed by immunostaining for Fos, the nuclear phosphoprotein product of the c-fos gene. In this study, we examined the effect of systemic morphine on Fos-like immunoreactivity (FLI) evoked in the formalin test, a widely used model of persistent pain. Awake rats received a subcutaneous 150 microliters injection of 5% formalin into the plantar aspect of the right hindpaw. The pattern of nuclear FLI was consistent with the known nociceptive primary afferent input from the hindpaw. Dense labeling was recorded in the superficial dorsal horn (laminae I and IIo) and in the neck of the dorsal horn (laminae V and VI), areas that contain large populations of nociceptive neurons. Sparse labeling was noted in lamina IIi and in the nucleus proprius (laminae III and IV), generally considered to be nonnociceptive areas of the cord. Fos immunoreactivity was also evoked in the ventromedial gray, including laminae VII, VIII, and X. There was no labeling in lamina IX of the ventral horn. Since FLI was time dependent and distributed over several spinal segments, we focused our analysis where maximal staining was found (L3-L5) and at the earliest time point of the peak Fos immunoreactivity (2 hr). Twenty minutes prior to the formalin injection, the rats received morphine (1.0, 2.5, 5.0, or 10 mg/kg, s.c.) or saline vehicle. Two hours later, the rats were killed, their spinal cords removed, and 50 microns transverse sections of the lumbar enlargement were immunostained with a rabbit polyclonal antiserum directed against Fos. Prior treatment with morphine sulfate profoundly suppressed formalin-evoked FLI in a dose-dependent and naloxone-reversible manner. The dose-response relationship of morphine-induced suppression of FLI varied in different laminae. To quantify the effect of morphine on FLI, labeled neurons in sections taken from the L4/5 level of each rat were plotted with a camera lucida and counted. Staining in the neck of the dorsal horn (laminae V and VI) and in more ventral laminae VII, VIII, and X, was profoundly suppressed by doses of morphine which also suppress formalin-evoked behavior. Although the labeling was also significantly reduced in laminae I and II, at the highest doses of morphine there was substantial residual labeling in the superficial dorsal horn. These data indicate that analgesia from systemic opiates involves differential regulation of nociceptive processing in subpopulations of spinal nociceptive neurons.


Quantitative analysis of antimicrobial use on British dairy farms.
Antimicrobial resistance has been reported to represent a growing threat to both human and animal health, and concerns have been raised around levels of antimicrobial usage (AMU) within the livestock industry. To provide a benchmark for dairy cattle AMU and identify factors associated with high AMU, data from a convenience sample of 358 dairy farms were analysed using both mass-based and dose-based metrics following standard methodologies proposed by the European Surveillance of Veterinary Antimicrobial Consumption project. Metrics calculated were mass (mg) of antimicrobial active ingredient per population correction unit (mg/PCU), defined daily doses (DDDvet) and defined course doses (DCDvet). AMU on dairy farms ranged from 0.36 to 97.79 mg/PCU, with a median and mean of 15.97 and 20.62 mg/PCU, respectively. Dose-based analysis ranged from 0.05 to 20.29 DDDvet, with a median and mean of 4.03 and 4.60 DDDvet, respectively. Multivariable analysis highlighted that usage of antibiotics via oral and footbath routes increased the odds of a farm being in the top quartile (>27.9 mg/PCU) of antimicrobial users. While dairy cattle farm AMU appeared to be lower than UK livestock average, there were a selection of outlying farms with extremely high AMU, with the top 25 per cent of farms contributing greater than 50 per cent of AMU by mass. Identification of these high use farms may enable targeted AMU reduction strategies and facilitate a significant reduction in overall dairy cattle AMU.


Structural Insights into the Distinct Binding Mode of Cyclic Di-AMP with SaCpaA_RCK.
Cyclic di-AMP (c-di-AMP) is a relatively new member of the family of bacterial cyclic dinucleotide second messengers. It has attracted significant attention in recent years because of the abundant roles it plays in a variety of Gram-positive bacteria. The structural features that allow diverse bacterial proteins to bind c-di-AMP are not fully understood. Here we report the biophysical and structural studies of c-di-AMP in complex with a bacterial cation-proton antiporter (CpaA) RCK (regulator of the conductance of K(+)) protein from Staphylococcus aureus (Sa). The crystal structure of the SaCpaA_RCK C-terminal domain (CTD) in complex with c-di-AMP was determined to a resolution of 1.81 Å. This structure revealed two well-liganded water molecules, each interacting with one of the adenine bases by a unique H2Olp-π interaction to stabilize the complex. Sequence blasting using the SaCpaA_RCK primary sequence against the bacterial genome database returned many CpaA analogues, and alignment of these sequences revealed that the active site residues are all well-conserved, indicating a universal c-di-AMP binding mode for CpaA_RCK. A proteoliposome activity assay using the full-length SaCpaA membrane protein indicated that c-di-AMP binding alters its antiporter activity by approximately 40%. A comparison of this structure to all other reported c-di-AMP-receptor complex structures revealed that c-di-AMP binds to receptors in either a "U-shape" or "V-shape" mode. The two adenine rings are stabilized in the inner interaction zone by a variety of CH-π, cation-π, backbone-π, or H2Olp-π interaction, but more commonly in the outer interaction zone by hydrophobic CH-π or π-π interaction. The structures determined to date provide an understanding of the mechanisms by which a single c-di-AMP can interact with a variety of receptor proteins, and how c-di-AMP binds receptor proteins in a special way different from that of c-di-GMP.


Improvement in cardiac structure and functions early after transcatheter closure of secundum atrial septal defect in children and adolescents.
We sought to assess the effects of transcatheter closure of atrial septal defect (ASD) on right and left ventricular form and functions, as well as atrial volumes and pulmonary venous flows. We enrolled 25 patients (mean age: 9.02) prospectively who underwent successful transcatheter closure of secundum ASD. We performed transthoracic echocardiography, including two-dimensional, pulsed wave Doppler, M-mode echocardiography, and tissue Doppler imaging before the procedure and 1 day, 1 month, 3 months and 6 months after the procedure. Serum brain natriuretic peptide (BNP) levels were measured prior to the procedure, and 1 day, 1 month, and 3 months there after. Mitral inflow early diastolic wave increased significantly, while isovolumetric relaxation time and deceleration time did not change during the follow-up. The E/E' was also increased significantly during follow-up. After the closure, right ventricular size and right atrial volume reduced, while left ventricular size increased significantly. There was a statistically significant improvement in left and right ventricular Tei indices. Pulmonary vein systolic velocity and the ratio of systolic to diastolic wave decreased, while atrial reversal wave (ARW) velocity increased immediately after the procedure. Although the concentration of BNP was increased on the first day after the procedure, its levels reduced and had reached the pre-procedure values at 1 month of follow-up. In the study, a significant improvement in the right and left ventricular functions was detected after transcatheter closure of secundum ASD in the short-term follow-up. In addition, we found a significant reduction in right heart sizes with corresponding global functional improvement in the right ventricle after the procedure.


Risk factors for sebaceous gland diseases and their relationship to gastrointestinal dysfunction in Han adolescents.
Sebaceous gland diseases are a group of common dermatological diseases with multiple causes. To date, a systematic report of the risk factors for sebaceous gland diseases in adolescents has not been published. The aim of this study was to assess the prevalence and risk factors for certain sebaceous gland diseases (seborrhea, seborrheic dermatitis, acne, androgenetic alopecia and rosacea) and their relationship to gastrointestinal dysfunction in adolescents. From August-October, 2002-2005, a questionnaire survey was carried out to obtain epidemiological data about sebaceous gland diseases. Using random cluster sampling, 13 215 Han adolescents aged 12-20 years were recruited from four countries or districts (Macau; Guangzhou, China; Malaysia; and Indonesia). The statistical software SPSS ver. 13.0 was used to analyze the data. The prevalence of seborrhea, seborrheic dermatitis, acne, androgenetic alopecia and rosacea was 28.27%, 10.17%, 51.03%, 1.65% and 0.97%, respectively. Based on multivariate logistic regression analysis, the risk factors for sebaceous gland diseases included: age; duration of local residency; halitosis; gastric reflux; abdominal bloating; constipation; sweet food; spicy food; family history of acne; late night sleeping on a daily basis; excessive axillary, body and facial hair; excessive periareolar hair; and anxiety. There was a statistically significant difference in the prevalence of gastrointestinal symptoms (halitosis; gastric reflux; abdominal bloating; constipation) between patients with and without sebaceous gland diseases (chi(2) = 150.743; P = 0.000). Gastrointestinal dysfunction is an important risk factor for diseases of the sebaceous glands and is correlated with their occurrence and development.


Comparison of the chloroplast peroxidase system in the chlorophyte Chlamydomonas reinhardtii, the bryophyte Physcomitrella patens, the lycophyte Selaginella moellendorffii and the seed plant Arabidopsis thaliana.
Oxygenic photosynthesis is accompanied by the formation of reactive oxygen species (ROS), which damage proteins, lipids, DNA and finally limit plant yield. The enzymes of the chloroplast antioxidant system are exclusively nuclear encoded. During evolution, plastid and mitochondrial genes were post-endosymbiotically transferred to the nucleus, adapted for eukaryotic gene expression and post-translational protein targeting and supplemented with genes of eukaryotic origin. Here, the genomes of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii and the seed plant Arabidopsis thaliana were screened for ORFs encoding chloroplast peroxidases. The identified genes were compared for their amino acid sequence similarities and gene structures. Stromal and thylakoid-bound ascorbate peroxidases (APx) share common splice sites demonstrating that they evolved from a common ancestral gene. In contrast to most cormophytes, our results predict that chloroplast APx activity is restricted to the stroma in Chlamydomonas and to thylakoids in Physcomitrella. The moss gene is of retrotransposonal origin.The exon-intron-structures of 2CP genes differ between chlorophytes and streptophytes indicating an independent evolution. According to amino acid sequence characteristics only the A-isoform of Chlamydomonas 2CP may be functionally equivalent to streptophyte 2CP, while the weakly expressed B- and C-isoforms show chlorophyte specific surfaces and amino acid sequence characteristics. The amino acid sequences of chloroplast PrxII are widely conserved between the investigated species. In the analyzed streptophytes, the genes are unspliced, but accumulated four introns in Chlamydomonas. A conserved splice site indicates also a common origin of chlorobiont PrxQ.The similarity of splice sites also demonstrates that streptophyte glutathione peroxidases (GPx) are of common origin. Besides a less related cysteine-type GPx, Chlamydomonas encodes two selenocysteine-type GPx. The latter were lost prior or during streptophyte evolution. Throughout plant evolution, there was a strong selective pressure on maintaining the activity of all three investigated types of peroxidases in chloroplasts. APx evolved from a gene, which dates back to times before differentiation of chlorobionts into chlorophytes and streptophytes, while Prx and presumably also GPx gene patterns may have evolved independently in the streptophyte and chlorophyte branches.


Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase.
Heme catalases prevent cells from oxidative damage by decomposing hydrogen peroxide into water and molecular oxygen. Here we investigate the factors that give rise to an undesirable side reaction competing with normal catalase activity, the migration of a radical from the heme active site to the protein in the principal reaction intermediate compound I (Cpd I). Recently, it has been proposed that this electron transfer reaction takes place in Cpd I of Helicobacter pylori catalase (HPC), but not in Cpd I of Penicillium vitale catalase (PVC), where the oxidation equivalent remains located on the heme active site. Unraveling the factors determining the different radical locations could help engineer enzymes with enhanced catalase activity for detection or removal of hydrogen peroxide. Using quantum mechanics/molecular mechanics metadynamics simulations, we show that radical migration in HPC is facilitated by the large driving force (-0.65 eV) of the subsequent proton transfer from a histidine residue to the ferryl oxygen atom of reduced Cpd I. The corresponding free energy in PVC is significantly smaller (-0.19 eV) and, as we argue, not sufficiently high to support radical migration. Our results suggest that the energetics of oxoferryl protonation is a key factor regulating radical migration in catalases and possibly also in hydroperoxidases.


Extending the definition of the GyrB quinolone resistance-determining region in Mycobacterium tuberculosis DNA gyrase for assessing fluoroquinolone resistance in M. tuberculosis.
Fluoroquinolone (FQ) resistance is emerging in Mycobacterium tuberculosis. The main mechanism of FQ resistance is amino acid substitution within the quinolone resistance-determining region (QRDR) of the GyrA subunit of DNA gyrase, the sole FQ target in M. tuberculosis. However, substitutions in GyrB whose implication in FQ resistance is unknown are increasingly being reported. The present study clarified the role of four GyrB substitutions identified in M. tuberculosis clinical strains, two located in the QRDR (D500A and N538T) and two outside the QRDR (T539P and E540V), in FQ resistance. We measured FQ MICs and also DNA gyrase inhibition by FQs in order to unequivocally clarify the role of these mutations in FQ resistance. Wild-type GyrA, wild-type GyrB, and mutant GyrB subunits produced from engineered gyrB alleles by mutagenesis were overexpressed in Escherichia coli, purified to homogeneity, and used to reconstitute highly active gyrase complexes. MICs and DNA gyrase inhibition were determined for moxifloxacin, gatifloxacin, ofloxacin, levofloxacin, and enoxacin. All these substitutions are clearly implicated in FQ resistance, underlining the presence of a hot spot region housing most of the GyrB substitutions implicated in FQ resistance (residues NTE, 538 to 540). These findings help us to refine the definition of GyrB QRDR, which is extended to positions 500 to 540.


A longitudinal examination of dyadic distress patterns following a skills intervention for carers of adolescents with anorexia nervosa.
Family interventions in anorexia nervosa (AN) have been developed to ameliorate maladaptive patterns of patient-carer interaction that can play a role in illness maintenance. The primary aim of this study is to examine the inter-relationship between baseline and post-treatment distress in dyads of carers and patients with AN to examine the interdependence between carers and patients. The secondary aim is to examine whether a carer skills intervention [Experienced Carer Helping Others (ECHO)] impacts on this inter-relationship. Dyads consisting of treatment-seeking adolescents with AN and their primary carer (n = 149; mostly mothers) were randomised to receive a carer skills intervention (ECHO) in addition to treatment as usual (TAU), or TAU alone, as part of a larger clinical trial. Carers and patients completed a standardised measure of psychological distress (The Depression, Anxiety, and Stress Scale) at baseline and 12 months post-treatment. The Actor Partner Interdependence Model was used to examine longitudinal changes in interdependence by treatment group. As expected, post-treatment levels of distress were related to baseline levels in both groups (actor effects). Moreover, carer distress at 12 months was related to patient distress at baseline for the TAU (partner effects), but not for the ECHO group. Finally, carers' distress change was not a significant predictor of patients' body mass index (BMI) change in the two treatment conditions. These findings are limited to predominantly mother-offspring dyads and may not generalise to other relationships. The ECHO intervention which is designed to teach carers skills in illness management and emotion regulation may be an effective addition to TAU for ameliorating interdependence of distress in patients and their primary carers over time.


Genetic Characterization of a Recombinant Myxoma Virus in the Iberian Hare (Lepus granatensis).
Myxomatosis is a lethal disease in wild European and domestic rabbits (Oryctolagus cuniculus), which is caused by a Myxoma virus (MYXV) infection-a leporipoxvirus that is found naturally in some Sylvilagus rabbit species in South America and California. The introduction of MYXV into feral European rabbit populations of Australia and Europe, in the early 1950s, demonstrated the best-documented field example of host-virus coevolution, following a cross-species transmission. Recently, a new cross-species jump of MYXV has been suggested in both Great Britain and Spain, where European brown hares (Lepus europaeus) and Iberian hares (Lepus granatensis) were found dead with lesions consistent with those observed in myxomatosis. To investigate the possibility of a new cross-species transmission event by MYXV, tissue samples collected from a wild Iberian hare found dead in Spain (Toledo region) were analyzed and deep sequenced. Our results reported a new MYXV isolate (MYXV Toledo) in the tissues of this species. The genome of this new virus was found to encode three disruptive genes (M009L, M036L, and M152R) and a novel ~2.8 kb recombinant region, which resulted from an insertion of four novel poxviral genes towards the 3' end of the negative strand of its genome. From the open reading frames inserted into the MYXV Toledo virus, a new orthologue of a poxvirus host range gene family member was identified, which was related to the MYXV gene M064R. Overall, we confirmed the identity of a new MYXV isolate in Iberian hares, which, we hypothesized, was able to more effectively counteract the host defenses in hares and start an infectious process in this new host.


Self-assembled materials and supramolecular chemistry within microfluidic environments: from common thermodynamic states to non-equilibrium structures.
Self-assembly is a crucial component in the bottom-up fabrication of hierarchical supramolecular structures and advanced functional materials. Control has traditionally relied on the use of encoded building blocks bearing suitable moieties for recognition and interaction, with targeting of the thermodynamic equilibrium state. On the other hand, nature leverages the control of reaction-diffusion processes to create hierarchically organized materials with surprisingly complex biological functions. Indeed, under non-equilibrium conditions (kinetic control), the spatio-temporal command of chemical gradients and reactant mixing during self-assembly (the creation of non-uniform chemical environments for example) can strongly affect the outcome of the self-assembly process. This directly enables a precise control over material properties and functions. In this tutorial review, we show how the unique physical conditions offered by microfluidic technologies can be advantageously used to control the self-assembly of materials and of supramolecular aggregates in solution, making possible the isolation of intermediate states and unprecedented non-equilibrium structures, as well as the emergence of novel functions. Selected examples from the literature will be used to confirm that microfluidic devices are an invaluable toolbox technology for unveiling, understanding and steering self-assembly pathways to desired structures, properties and functions, as well as advanced processing tools for device fabrication and integration.


Crystalline camptothecin-20(S)-O-propionate hydrate: a novel anticancer agent with strong activity against 19 human tumor xenografts.
To find a more effective and less toxic chemotherapeutic agent, we have successfully prepared crystalline camptothecin-20(S)-O-propionate hydrate (CZ48) by reacting camptothecin with propionic anhydride using concentrated sulfuric acid as catalyst. The biological effectiveness of this new anticancer agent was evaluated by using xenografts of human cancers in nude mice as the testing models. The extensive treatment of 21 human tumors with various dose levels of CZ48 has shown that this agent is highly effective against many different human tumors tested with a striking lack of toxicity. Of the 21 human tumor lines tested, 9 regressed, 5 were <10% of the control, 3 were <20%, and 2 were <40%. Two tumors did not respond. The total response rate was 90% (19 of 21). No toxicity was observed in mice. The effective doses required to achieve the positive response varied from 100 to 1,000 mg/kg/d depending on the tumors. The maximum tolerated dose was not reached because of the nontoxic nature of the drug in mice. Thus, this compound has a much wider therapeutic index compared with that of the existing anticancer drugs currently in use.


Inherited resistance to arsenate toxicity in two populations of Lumbricus rubellus.
No unequivocal evidence exists of genetically inherited resistance to metals/metalloids in field populations of earthworms. We studied cocoon production in adult Lumbricus rubellus Hoffmeister collected from an abandoned arsenic and copper mine (Devon Great Consols, Devon, UK), and abandoned tungsten mine (Carrock Fell, Cumbria, UK) and an uncontaminated cultured population. The earthworms were kept in uncontaminated soil for nine weeks. From a total of 42 L. rubellus from each site, Devon Great Consols adults produced 301 cocoons, of which 42 were viable; Carrock Fell 60 cocoons, of which 11 were viable; and the reference population 101 cocoons, of which 62 were viable. The hatchlings were collected and stored at 4 degrees C at weekly intervals. After 12 weeks, all hatchlings were transferred to clean soil and maintained at 15 degrees C for 20 weeks until they showed evidence of a clitellum. In toxicity trials, F1 generation L. rubellus were exposed to 2,000 mg As/kg as sodium arsenate or 300 mg Cu/kg as copper chloride for 28 d. The F1 generation L. rubellus from Devon Great Consols mine demonstrated resistance to arsenate but not copper. All L. rubellus from Devon Great Consols kept in soil treated with sodium arsenate remained in good condition over the 28-d period but lost condition rapidly and suffered high mortality in soil treated with copper chloride. The control population suffered high mortality in soil treated with sodium arsenate and copper chloride. Previous work has shown that field-collected adults demonstrate resistance to both arsenate and Cu toxicity under these conditions. Thus, while arsenate resistance may be demonstrated in F1 generation L. rubellus from one of the contaminated sites, Cu resistance is not. The F1 adults and F2 cocoons did not have significantly higher levels of As than the control population, with no residual As tissue burden, suggesting that resistance to As in these populations may be inherited.


HyDRA: gene prioritization via hybrid distance-score rank aggregation.
Gene prioritization refers to a family of computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the training set, and the rankings of genes under various similarity criteria are aggregated via statistical methods. The contributions of our work are threefold: (i) first, based on the realization that there is no unique way to define an optimal aggregate for rankings, we investigate the predictive quality of a number of new aggregation methods and known fusion techniques from machine learning and social choice theory. Within this context, we quantify the influence of the number of training genes and similarity criteria on the diagnostic quality of the aggregate and perform in-depth cross-validation studies; (ii) second, we propose a new approach to genomic data aggregation, termed HyDRA (Hybrid Distance-score Rank Aggregation), which combines the advantages of score-based and combinatorial aggregation techniques. We also propose incorporating a new top-versus-bottom (TvB) weighting feature into the hybrid schemes. The TvB feature ensures that aggregates are more reliable at the top of the list, rather than at the bottom, since only top candidates are tested experimentally; (iii) third, we propose an iterative procedure for gene discovery that operates via successful augmentation of the set of training genes by genes discovered in previous rounds, checked for consistency. Fundamental results from social choice theory, political and computer sciences, and statistics have shown that there exists no consistent, fair and unique way to aggregate rankings. Instead, one has to decide on an aggregation approach using predefined set of desirable properties for the aggregate. The aggregation methods fall into two categories, score- and distance-based approaches, each of which has its own drawbacks and advantages. This work is motivated by the observation that merging these two techniques in a computationally efficient manner, and by incorporating additional constraints, one can ensure that the predictive quality of the resulting aggregation algorithm is very high. We tested HyDRA on a number of gene sets, including autism, breast cancer, colorectal cancer, endometriosis, ischaemic stroke, leukemia, lymphoma and osteoarthritis. Furthermore, we performed iterative gene discovery for glioblastoma, meningioma and breast cancer, using a sequentially augmented list of training genes related to the Turcot syndrome, Li-Fraumeni condition and other diseases. The methods outperform state-of-the-art software tools such as ToppGene and Endeavour. Despite this finding, we recommend as best practice to take the union of top-ranked items produced by different methods for the final aggregated list. The HyDRA software may be downloaded from: http://web.engr.illinois.edu/∼mkim158/HyDRA.zip. Supplementary data are available at Bioinformatics online.


A population-based study of cardiac morbidity among Hodgkin lymphoma patients with preexisting heart disease.
The risk of cardiac hospitalization (CH) in Hodgkin lymphoma (HL) patients with preexisting heart disease was evaluated. Patients with HL were identified from a population-based registry (N = 3964). Data were abstracted from records of a randomly selected subcohort (N = 1096). A population-based registry was used to identify CH. Factors associated with CH and the incidence of CH after HL were estimated with competing risk models. Preexisting heart disease was the strongest predictor of posttreatment CH (hazard ratio = 3.98, P < .001) and significantly modified (P = .01) the effect of treatment on the risk of CH. Among patients with preexisting heart disease, treatment with mediastinal radiation therapy plus doxorubicin-based chemotherapy was associated with a 10-year incidence of CH more than 20% higher than treatment with chemotherapy alone. There is a high risk of CH after mediastinal radiation therapy plus doxorubicin-based chemotherapy among patients with preexisting heart disease; this is an important consideration when weighing treatment options, and in the follow-up of these patients.


An on-demand femtoliter droplet dispensing system based on a gigahertz acoustic resonator.
On-demand droplet dispensing systems are indispensable tools in bioanalytical fields, such as microarray fabrication. Biomaterial solutions can be very limited and expensive, so minimizing the use of solution per spot produced is highly desirable. Here, we proposed a novel droplet dispensing method which utilizes a gigahertz (GHz) acoustic resonator to deposit well-defined droplets on-demand. This ultra-high frequency acoustic resonator induces a highly localized and strong body force at the solid-liquid interface, which pushes the liquid to generate a stable and sharp "liquid needle" and further delivers droplets to the target substrate surface by transient contact. This approach is between contact and non-contact methods, thus avoiding some issues of traditional methods (such as nozzle clogging or satellite spots). We demonstrated the feasibility of this approach by fabricating high quality DNA and protein microarrays on glass and flexible substrates. Notably, the spot size can be delicately controlled down to a few microns (femtoliter in volume). Because of the CMOS compatibility, we expect this technique to be readily applied to advanced biofabrication processes.


Perineural Invasion and Risk of Lethal Prostate Cancer.
Background: Prostate cancer has a propensity to invade and grow along nerves, a phenomenon called perineural invasion (PNI). Recent studies suggest that the presence of PNI in prostate cancer has been associated with cancer aggressiveness.Methods: We investigated the association between PNI and lethal prostate cancer in untreated and treated prostate cancer cohorts: the Swedish Watchful Waiting Cohort of 615 men who underwent watchful waiting, and the U.S. Health Professionals Follow-Up Study of 849 men treated with radical prostatectomy. One pathologist performed a standardized histopathologic review assessing PNI and Gleason grade. Patients were followed from diagnosis until metastasis or death.Results: The prevalence of PNI was 7% and 44% in the untreated and treated cohorts, respectively. PNI was more common in high Gleason grade tumors in both cohorts. PNI was associated with enhanced tumor angiogenesis, but not tumor proliferation or apoptosis. In the Swedish study, PNI was associated with lethal prostate cancer [OR 7.4; 95% confidence interval (CI), 3.6-16.6; P < 0.001]. A positive, although not statistically significant, association persisted after adjustment for age, Gleason grade, and tumor volume (OR 1.9; 95% CI, 0.8-5.1; P = 0.17). In the U.S. study, PNI predicted lethal prostate cancer independent of clinical factors (HR 1.8; 95% CI, 1.0, 3.3; P =0.04).Conclusions: These data support the hypothesis that perineural invasion creates a microenvironment that promotes cancer aggressiveness.Impact: Our findings suggest that PNI should be a standardized component of histopathologic review, and highlights a mechanism underlying prostate cancer metastasis. Cancer Epidemiol Biomarkers Prev; 26(5); 719-26. ©2017 AACR.


Integrated analysis of telomerase enzymatic activity unravels an association with cancer stemness and proliferation.
Active telomerase is essential for stem cells and most cancers to maintain telomeres. The enzymatic activity of telomerase is related but not equivalent to the expression of TERT, the catalytic subunit of the complex. Here we show that telomerase enzymatic activity can be robustly estimated from the expression of a 13-gene signature. We demonstrate the validity of the expression-based approach, named EXTEND, using cell lines, cancer samples, and non-neoplastic samples. When applied to over 9,000 tumors and single cells, we find a strong correlation between telomerase activity and cancer stemness. This correlation is largely driven by a small population of proliferating cancer cells that exhibits both high telomerase activity and cancer stemness. This study establishes a computational framework for quantifying telomerase enzymatic activity and provides new insights into the relationships among telomerase, cancer proliferation, and stemness.


Oldest known dinosaurian nesting site and reproductive biology of the Early Jurassic sauropodomorph Massospondylus.
The extensive Early Jurassic continental strata of southern Africa have yielded an exceptional record of dinosaurs that includes scores of partial to complete skeletons of the sauropodomorph Massospondylus, ranging from embryos to large adults. In 1976 an incomplete egg clutch including in ovo embryos of this dinosaur, the oldest known example in the fossil record, was collected from a road-cut talus, but its exact provenance was uncertain. An excavation program at the site started in 2006 has yielded multiple in situ egg clutches, documenting the oldest known dinosaurian nesting site, predating other similar sites by more than 100 million years. The presence of numerous clutches of eggs, some of which contain embryonic remains, in at least four distinct horizons within a small area, provides the earliest known evidence of complex reproductive behavior including site fidelity and colonial nesting in a terrestrial vertebrate. Thus, fossil and sedimentological evidence from this nesting site provides empirical data on reproductive strategies in early dinosaurs. A temporally calibrated optimization of dinosaurian reproductive biology not only demonstrates the primary significance of the Massospondylus nesting site, but also provides additional insights into the initial stages of the evolutionary history of dinosaurs, including evidence that deposition of eggs in a tightly organized single layer in a nest evolved independently from brooding.


In situ effective diffusion coefficient profiles in live biofilms using pulsed-field gradient nuclear magnetic resonance.
Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface-averaging methods are used, position-dependent measurements of the effective diffusion coefficient are currently: (1) invasive to the biofilm, (2) performed under unnatural conditions, (3) lethal to cells, and/or (4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate results and prohibit further (time-dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: (1) measure the effective diffusion coefficient for water in live biofilms, (2) monitor how the effective diffusion coefficient changes over time under growth conditions, and (3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two-dimensional effective diffusion coefficient maps within Shewanella oneidensis MR-1 biofilms using pulsed-field gradient nuclear magnetic resonance methods, and used them to calculate surface-averaged relative effective diffusion coefficient (D(rs)) profiles. We found that (1) D(rs) decreased from the top of the biofilm to the bottom, (2) D(rs) profiles differed for biofilms of different ages, (3) D(rs) profiles changed over time and generally decreased with time, (4) all the biofilms showed very similar D(rs) profiles near the top of the biofilm, and (5) the D(rs) profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm.


Transcriptomic analyses of the anti-adipogenic effects of oleuropein in human mesenchymal stem cells.
Extra virgin olive oil has positive effects on health. Oleuropein is a polyphenolic compound present in olive-tree leaves, fruits (olives) and olive oil. It is responsible for the relevant organoleptic and biological properties of olive oil, including antiadipogenic properties. Thus, the effects of oleuropein on the adipogenesis of human bone-marrow mesenchymal stem cells were studied by transcriptomics and differential gene-expression analyses. Oleuropein could upregulate expression of 60% of adipogenesis-repressed genes. Besides, it could activate signaling pathways such as Rho and β-catenin, maintaining cells at an undifferentiated stage. Our data suggest that mitochondrial activity is reduced by oleuropein, mostly during adipogenic differentiation. These results shed light on oleuropein activity on cells, with potential application as a "nutraceutical" for the prevention and treatment of diseases such as obesity and osteoporosis.


Women outperform men in remembering to remember.
The study of gender differences in prospective memory (i.e., remembering to remember) has received modest attention in the literature. The few reported studies investigating either subjective or objective evaluations of prospective memory have shown inconsistent data. In this study, we aimed to verify the presence of gender differences during the performance of an objective prospective memory test by considering the weight of specific variables such as length of delay, type of response, and type of cue. We submitted a sample of 100 healthy Italian participants (50 men and 50 women) to a test expressly developed to assess prospective memory: The Memory for Intentions Screening Test. Women performed better than men in remembering to do an event-based task (i.e., prompted by an external event) and when the task required a physical response modality. We discuss the behavioural differences that emerged by considering the possible role of sociological, biological, neuroanatomical, and methodological variables.


Regeneration of Leydig cells in ectopically autografted adult mouse testes.
Ectopic autografting of testis tissue is a promising approach for studying testicular development, male germline preservation and restoration of male fertility. In this study, we examined the fate of various testicular cells in adult mouse testes following ectopic autografting at 1, 2, 4 and 8 weeks post grafting. Histological examination showed no evidence of re-establishment of spermatogenesis in autografts, and progressive degeneration of seminiferous tubules was detected. Expression of germ cell-specific proteins such as POU5F1, DAZL, TNP1, TNP2, PRM1 and PRM2 revealed that, although proliferating and differentiating spermatogenic germ cells such as spermatogonia, spermatocytes and spermatids could survive in autografts until 4 weeks, only terminally differentiated germ cells such as sperm persisted in autografts until 8 weeks. The presence of Sertoli and peritubular myoid cells, as indicated by expression of WT1 and ACTA2 proteins, respectively, was evident in the autografts until 8 weeks. Interestingly, seminal vesicle weight and serum testosterone level were restored in autografted mice by 8 weeks post grafting. The expression of Leydig cell-specific proteins such as CYP11A1, HSD3B2 and LHCGR showed revival of Leydig cell (LC) populations in autografts over time since grafting. Elevated expression of PDGFRA, LIF, DHH and NEFH in autografts indicated de novo regeneration of LC populations. Autografted adult testis can be used as a model for investigating Leydig cell regeneration, steroidogenesis and regulation of the intrinsic factors involved in Leydig cell development. The success of this rodent model can have therapeutic applications for adult human males undergoing sterilizing cancer therapy.


Home practice in Mindfulness-Based Cognitive Therapy and Mindfulness-Based Stress Reduction: A systematic review and meta-analysis of participants' mindfulness practice and its association with outcomes.
Mindfulness-Based Cognitive Therapy (MBCT) and Mindfulness-Based Stress Reduction (MBSR) emphasize the importance of mindfulness practice at home as an integral part of the program. However, the extent to which participants complete their assigned practice is not yet clear, nor is it clear whether this practice is associated with positive outcomes. For this systematic review and meta-analysis, searches were performed using Scopus and PubMed for studies published through to the end of 2015, reporting on formal home practice of mindfulness by MBSR or MBCT participants. Across 43 studies (N = 1427), the pooled estimate for participants' home practice was 64% of the assigned amount, equating to about 30 minutes per day, six days per week [95% CI 60-69%]. There was substantial heterogeneity associated with this estimate. Across 28 studies (N = 898), there was a small but significant association between participants' self-reported home practice and intervention outcomes (r = 0·26, 95% CI 0·19,-0·34). MBSR and MBCT participants report completing substantial formal mindfulness practice at home over the eight-week intervention, albeit less than assigned amounts. There is a small but significant association between the extent of formal practice and positive intervention outcomes for a wide range of participants.


Predictors of Retention in an Alcohol and Risky Sex Prevention Program for Homeless Young Adults.
Homeless young adults are at risk for alcohol and other drug (AOD) use and risky sexual behavior. Interventions are needed to help these young people reduce their risky behavior, but this population is often difficult to engage and retain in services. We offered a four-session AOD and risky sex reduction program to 100 participants and examined if retention in the program was predicted by a number of factors: demographics, homelessness severity, other service use, AOD behaviors, mental health symptoms, sexual risk behaviors, and readiness to change AOD and condom use. Nearly half (48%) of participants completed all sessions. In bivariate analyses, participants were significantly less likely to be retained in the program if they had slept outdoors in the past month, engaged in more alcohol and marijuana use, experienced more alcohol-related consequences, and received the program in an urban drop-in center (as opposed to a drop-in center near the beach). When controlling for all significant bivariate relationships, only sleeping outdoors and receipt of the program in the urban setting predicted fewer sessions completed. The most endorsed reasons for program non-completion were being too busy to attend and inconvenient day/time of the program. Findings can help outreach staff and researchers better prepare methods to engage higher risk homeless youth and retain them in services. Finding unique ways to help youth overcome barriers related to location of services appears especially necessary, perhaps by bringing services to youth where they temporarily reside or offering meaningful incentives for program attendance.


PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.
Although several tools for the analysis of ChIP-seq data have been published recently, there is a growing demand, in particular in the plant research community, for computational resources with which such data can be processed, analyzed, stored, visualized and integrated within a single, user-friendly environment. To accommodate this demand, we have developed PRI-CAT (Plant Research International ChIP-seq analysis tool), a web-based workflow tool for the management and analysis of ChIP-seq experiments. PRI-CAT is currently focused on Arabidopsis, but will be extended with other plant species in the near future. Users can directly submit their sequencing data to PRI-CAT for automated analysis. A QuickLoad server compatible with genome browsers is implemented for the storage and visualization of DNA-binding maps. Submitted datasets and results can be made publicly available through PRI-CAT, a feature that will enable community-based integrative analysis and visualization of ChIP-seq experiments. Secondary analysis of data can be performed with the aid of GALAXY, an external framework for tool and data integration. PRI-CAT is freely available at http://www.ab.wur.nl/pricat. No login is required.


Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.
• Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.• We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.• Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.• We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales.


Quality evaluation and future priorities for delivering acute myocardial infarction care in Sri Lanka.
This study evaluates the quality of care for patients admitted with acute myocardial infarction (AMI) in a tertiary hospital in Colombo using the European Society of Cardiology Quality of Care Working Group's guidelines (2017). A recently implemented electronic AMI registry m-Health tool was used for prospective data collection. Each patient was assessed for eligibility for each of the six domains of quality. Global Registry of Acute Coronary Events Risk Model for predicted probability of mortality, and scores for risk of bleeding complications (CRUSADE) and severity of heart failure (Killip classification) were calculated as per published guidelines. A composite measure of quality was derived from compliance with the six domains. Patients were followed up via telephone at 30 days following discharge to evaluate outcome and satisfaction. Organisational information was assessed by administrative review and interview. Between March 2017 and April 2018, 934 patients with AMI presented to the cardiology department. The majority of patients (90.4%) presented with features of ST-elevation myocardial infarction (STEMI). Mean (SD) overall compliance with the composite quality indicator (CQI) was 44% (0.07). Compliance of ≥50% to the CQI was achieved in 9.8% of STEMI patients. The highest compliance was observed for antithrombotics during hospitalisation (79.1%) and continuous measure of patient satisfaction (76.1%). The lowest compliance was for organisational structure and care processes (22.4%). This study reports a registry-based continuous evaluation of the quality of AMI care from a low and middle-income country. Priorities for improvement include improved referral, and networking of primary and secondary health facilities with the percutaneous coronary intervention centre.


Integration to Implementation and the Micronutrient Forum: A Coordinated Approach for Global Nutrition. Case Study Application: Safety and Effectiveness of Iron Interventions.
Paramount among the challenges to our ability to address the role of food and nutrition in health promotion and disease prevention is how to design and implement context-specific interventions and guidance. The Integration to Effective Implementation (I-to-I) concept is intended to address the complexities of the global health context through engagement of the continuum of stakeholders involved in the food and nutrition enterprise. The 2014 Micronutrient Forum (MNF) Global Conference held in Addis Ababa, Ethiopia, in June 2014 offered the opportunity to apply the I-to-I approach with the use of current concerns about the safety and effectiveness of interventions to prevent and treat iron deficiency (ID) as a case study. ID is associated with a range of adverse outcomes, especially in pregnant and nonpregnant women, infants, and primary school-age children. Strategies to combat ID include iron supplementation, multiple micronutrient powders, and food-based interventions to enhance dietary iron intake. Recent reports indicate potential increased adverse risks when iron is provided in areas with high infection burdens (e.g., malaria). This paradox has weakened iron intervention programs. Furthermore, the selection and interpretation of available biomarkers for assessing iron nutrition have been found to be compromised by the inflammatory process. These issues highlight the need for a comprehensive approach that considers basic biology, assessment, interventions, and how these can be translated into appropriate programs and policies. The application of the I-to-I with the use of the MNF offered an opportunity to explore how that might be achieved.


Effects of bone marrow-derived mesenchymal stem cells and platelet-rich plasma on bone regeneration for osseointegration of dental implants: preliminary study in canine three-wall intrabony defects.
Tissue engineering has been applied to overcome the obstacles encountered with bone regeneration for the placement of dental implants. The purpose of this study was to determine the bone formation ability of human bone marrow-derived mesenchymal stem cells (BMMSCs) and platelet-rich plasma (PRP) when applied separately or together to the intrabony defect around dental implants with a porous hydroxyapatite (HA) scaffold. Standardized three-wall intrabony defects (4 × 4 × 4 mm) were created at the mesial of each dental implant site in four mongrel dogs. Defects were then grafted with the following materials: HA + BMMSCs (HS group), HA + PRP (HP group), HA + BMMSCs + PRP (HSP group), and HA scaffold alone (HA group). The level of bone formation (bone density) and osseointegration (bone-to-implant contact [BIC]) in bone defects around the implants were evaluated by histological and histometric analysis at 6 and 12 weeks after the placement of implants. HA, HS, HP, and HSP groups generally showed an increase in bone density and BIC between 6 and 12 weeks, except BIC in the HS group. Although no statistically significant differences were found among HA, HS, HP, and HSP groups (p > 0.05), the highest level of bone density and BIC were observed in the HSP group after the 12-week healing period. Furthermore, the level of bone maturation was higher in the HSP group than in the other groups as determined histologically. The findings of this preliminary study suggest that BMMSCs and PRP combined with HA scaffold may provide additional therapeutic effects on bone regeneration and improve osseointegration in bone defects around dental implants.


An observational study of functional abilities in infants, children, and adults with type 1 SMA.
To report cross-sectional clinical findings in a large cohort of patients affected by type 1 spinal muscular atrophy. We included 122 patients, of age ranging between 3 months and 22 years, 1 month. More than 70% (85/122) were older than 2 years and 25% (31/122) older than 10 years. Patients were classified according to the severity of phenotype and to the number of SMN2 copies. Patients with the more common and the most severe phenotype older than 2 years were, with few exceptions, on noninvasive ventilation and, with increasing age, more often had tracheostomy or >16-hour ventilation and a gastrostomy inserted. In contrast, 25 of the 28 patients with the mildest phenotype older than 2 years had no need for tracheostomy or other ventilatory or nutritional support. In patients older than 2 years, the Children's Hospital of Philadelphia Infant Test of Neuromuscular Disorders scores were generally lower compared to those found in younger patients and showed distinct levels of functional abilities according to the severity of the phenotype. Similar findings were also observed on the Hammersmith Infant Neurological Examination. Our findings confirm that, after the age of 2 years, patients with type 1 spinal muscular atrophy generally survive only if they have gastrostomy and tracheostomy or noninvasive ventilation >16 hours and have low scores on the functional scales. More variability, however, can be expected in those with the mildest phenotype, who achieve head control. These data provide important baseline information at the time treatments are becoming available.


Self-efficacy as an appraisal that moderates the coping-emotion relationship: associations among people with rheumatoid arthritis.
The way a coping strategy is expressed might depend on the nature of underlying efficacy expectations. For example, a cognitive coping strategy may have different content depending on efficacy beliefs underpinning the strategy's formulation and application. As such, self-efficacy (SE), as an appraisal, may moderate relationships between coping and outcomes: coping effects may differ depending on SE. This process was examined in 127 rheumatoid arthritis patients attending routine patient education/self-management programmes. Participants completed questionnaire measures of SE, coping, anxiety and depression at baseline and at 8 weeks follow-up. Regression analyses focused on coping and SE change variables, and their concurrent association with measures of change in anxiety and depression. Results highlighted contributions to these emotional variables from interactions between coping and SE. The nature of associations between coping and emotional outcomes was found to differ according to efficacy appraisals. This may have implications for clinical practice in that the adaptive significance of adjustment efforts may differ according to underlying SE.


Regression discontinuity threshold optimization.
Treatments often come with thresholds, e.g. we are given statins if our cholesterol is above a certain threshold. But which statin administration threshold maximizes our quality of life adjusted years? More generally, which threshold would optimize the average expected outcome? Regression discontinuity approaches are used to measure the local average treatment effect (LATE) and more recently also the Marginal Threshold Treatment Effect (MTTE), which shows how marginal changes in the threshold can affect the LATE. We extend this idea to define the problem of optimizing a policy threshold, i.e. selecting a threshold that optimizes the cumulative effect of the treatment on the treated. We present an estimator of the optimal threshold based on a constrained optimization framework. We show how to use machine learning (Gaussian process regression) for non-linear estimation. We also extend the estimation to a conservative threshold that is unlikely to produce harm, and we show how to include policy cost constraints. We apply these results to estimate an optimal tip-maximizing threshold for tip suggestions in taxi cabs Haggag (2014).


The importance of social sources of cigarettes to school students.
To discover the importance of social sources of tobacco to young people as opposed to commercial sources; to describe the peer market for cigarettes in schools and the consequences for young people of their involvement in it. Cross sectional questionnaire survey, one-to-one interviews, and focus groups. Seven schools in Birmingham, UK. All students in two randomly selected classes from each school completed the questionnaire, and never smokers, occasional smokers, and regular smokers were interviewed. Two thirds of occasional smokers and one quarter of regular smokers obtained cigarettes socially, mostly for free. A few smokers regularly bought their cigarettes from others. Among friendship groups, both smokers and non-smokers were involved in the exchange of cigarettes, often for money, which is a common activity. A few young people use the selling of cigarettes to fund their own smoking. Some young people, smokers and non-smokers, are involved in semi-commercial selling of cigarettes. All school students are aware of where to purchase cigarettes from non-friends, which is only used "in emergency" because of the high price. One school had a strong punishment policy for students caught with cigarettes. In this school, more people bought singles from the peer market and the price was higher. The passing and selling of cigarettes in school is a common activity, which from the young persons perspective, ensures that all share cross counter purchases. A few people are prepared to use the peer market for monetary gain and it appears to be responsive to external conditions. The peer market might mean that efforts to control illegal sales of cigarettes are not as effective as hoped.


A prospective cohort study on severe pain as a risk factor for long-term sickness absence in blue- and white-collar workers.
To estimate the impact of pain in different body regions on future long-term sickness absence (LTSA) among blue- and white-collar workers. Prospective cohort study in a representative sample of 5603 employees (the Danish Work Environment Cohort Study) interviewed in 2000, and followed in 2001-2002 in a national sickness absence register. Cox regression analysis was performed to assess the risk estimates of mutually adjusted severe pain in the neck/shoulder, low back, hand/wrist and knees for onset of LTSA, defined as receiving sickness absence compensation for at least 3 consecutive weeks. Age, gender, body mass index, smoking and diagnosed disease were controlled for. In 2000 the prevalence among blue- and white-collar workers, respectively, of severe pain was 33% and 29% (neck/shoulder), 33% and 25% (low back), 16% and 11% (hand/wrists), and 16% and 12% (knees). During 2001-2002, the prevalence of LTSA among blue- and white-collar workers was 18% and 12%, respectively. Hand/wrist pain (HR 1.49, 95% CI 1.23 to 1.81) and low back pain (HR 1.30, 95% CI 1.11 to 1.53) were significant risk factors among the total cohort. Neck/shoulder pain was a significant risk factor among white-collar workers only (HR 1.35, 95% CI 1.21 to 1.85). Knee pain was not a significant risk factor. While hand/wrist pain and low back pain are general risk factors for LTSA, neck/shoulder pain is a specific risk factor among white-collar workers. This study suggests the potential for preventing future LTSA through interventions to manage or reduce musculoskeletal pain.


Survey of ASCO members on management of sentinel node micrometastases in breast cancer: variation in treatment recommendations according to specialty.
American Society of Clinical Oncology (ASCO) guidelines recommend axillary dissection (ALND) as the primary treatment for sentinel node micrometastases (SNMM) in breast cancer. We hypothesized that variation exists in adherence to these guidelines and management of SNMM as a result of the medical specialty of the treating physician. A questionnaire was e-mailed to 2511 active members of ASCO who specialize in breast cancer and who are board certified in surgery, medical oncology, or radiation oncology. Questions covered treatment of SNMM and factors influencing clinical decisions. Survey responses were analyzed by the Kruskal-Wallis and Fisher's exact test. Of 612 questionnaires viewed by recipients, 537 (88%) were completed by 382 medical oncologists, 100 surgeons, and 55 radiation oncologists. Most (98.5%) regarded SNMM as clinically important. Unexpectedly, ALND for SNMM was recommended by only 23% of surgeons, 23% of medical oncologists, and 15% of radiation oncologists (no statistically significant intergroup difference). Factors identified as important in selecting patients for ALND were tumor size, age, tumor grade, lymphovascular invasion, and size of metastases. Most respondents in each specialty (89% overall) would consider adjuvant chemotherapy for primary tumors <1 cm if SNMM were present. Tumor size, age, size of metastases, estrogen receptor/progesterone receptor status, HER-2 neu status, and gene expression profile would influence this decision. Radiation oncologists (76%) were more likely than medical oncologists (57%) or surgeons (47%) to consider axillary radiation instead of ALND for SNMM (P = 0.0021). Guidelines recommending ALND for SNMM are not being followed by most of the ASCO members we surveyed.


Borrelia persica infection in dogs and cats: clinical manifestations, clinicopathological findings and genetic characterization.
Relapsing fever (RF) is an acute infectious disease caused by arthropod-borne spirochetes of the genus Borrelia. The disease is characterized by recurrent episodes of fever that concur with spirochetemia. The RF borrelioses include louse-borne RF caused by Borrelia recurrentis and tick-borne endemic RF transmitted by argasid soft ticks and caused by several Borrelia spp. such as B. crocidurae, B. coriaceae, B. duttoni, B. hermsii, B. hispanica and B. persica. Human infection with B. persica is transmitted by the soft tick Ornithodoros tholozani and has been reported from Iran, Israel, Egypt, India, and Central Asia. During 2003-2015, five cats and five dogs from northern, central and southern Israel were presented for veterinary care and detected with borrelia spirochetemia by blood smear microscopy. The causative infective agent in these animals was identified and characterized by PCR from blood and sequencing of parts of the flagellin (flab), 16S rRNA and glycerophosphodiester phosphodiestrase (GlpQ) genes. All animals were infected with B. persica genetically identical to the causative agent of human RF. Phylogenetic analysis indicated that DNA sequences from these pet carnivores clustered together with B. persica genotypes I and II from humans and O. tholozani ticks and distinctly from other RF Borrelia spp. The main clinical findings in cats included lethargy, anorexia, anemia in 5/5 cats and thrombocytopenia in 4/5. All dogs were lethargic and anorectic, 4/5 were febrile and anemic and 3/5 were thrombocytopenic. Three dogs were co-infected with Babesia spp. The animals were all treated with antibiotics and the survival rate of both dogs and cats was 80 %. The cat and dog that succumbed to disease died one day after the initiation of antibiotic treatment, while survival in the others was followed by the rapid disappearance of spirochetemia. This is the first report of disease due to B. persica infection in cats and the first case series in dogs. Infection was associated with anemia and thrombocytopenia. Fever was more frequently observed in dogs than cats. Domestic canines and felines suffer from clinical disease due to B. persica infection and may also serve as sentinels for human infection.


Rapid method for electron tomographic reconstruction and three-dimensional modeling of the murine synapse using an automated fiducial marker-free system.
Electron tomography (ET) has recently afforded new insights into neuronal architecture. However, the tedious process of sample preparation, image acquisition, alignment, back projection, and additional segmentation process of ET repels beginners. We have tried Hitachi's commercial packages integrated with a Hitachi H-7650 TEM to examine the potential of using an automated fiducial-less approach for our own neuroscience research. Semi-thick sections (200-300 nm) were cut from blocks of fixed mouse (C57BL) cerebellum and prepared for ET. Sets of images were collected automatically as each section was tilted by 2° increments (±60°). "Virtual" image volumes were computationally reconstructed in three dimension (3D) with the EMIP software using either the commonly used "weighted back-projection" (WBP) method or "topography-based reconstruction" (TBR) algorithm for comparison. Computed tomograms using the TBR were more precisely reconstructed compared with the WBP method. Following reconstruction, the image volumes were imported into the 3D editing software A-View and segmented according to synaptic organization. The detailed synaptic components were revealed by very thin virtual image slices; 3D models of synapse structure could be constructed efficiently. Overall, this simplified system provided us with a graspable tool for pursuing ET studies in neuroscience.


Intact crowding and temporal masking in dyslexia.
Phonological deficits in dyslexia are well documented. However, there is an ongoing discussion about whether visual deficits limit the reading skills of people with dyslexia. Here, we investigated visual crowding and backward masking. We presented a Vernier (i.e., two vertical bars slightly offset to the left or right) and asked observers to indicate the offset direction. Vernier stimuli are visually similar to letters and are strongly affected by crowding, even in the fovea. To increase task difficulty, Verniers are often followed by a mask (i.e., backward masking). We measured Vernier offset discrimination thresholds for the basic Vernier task, under crowding, and under backward masking, in students with dyslexia (n = 19) and age and intelligence matched students (n = 27). We found no group differences in any of these conditions. Controls with fast visual processing (good backward masking performance), were faster readers. By contrast, no such correlation was found among the students with dyslexia, suggesting that backward masking does not limit their reading efficiency. These findings indicate that neither elevated crowding nor elevated backward masking pose a bottleneck to reading skills of people with dyslexia.


Ontology based text mining of gene-phenotype associations: application to candidate gene prediction.
Gene-phenotype associations play an important role in understanding the disease mechanisms which is a requirement for treatment development. A portion of gene-phenotype associations are observed mainly experimentally and made publicly available through several standard resources such as MGI. However, there is still a vast amount of gene-phenotype associations buried in the biomedical literature. Given the large amount of literature data, we need automated text mining tools to alleviate the burden in manual curation of gene-phenotype associations and to develop comprehensive resources. In this study, we present an ontology-based approach in combination with statistical methods to text mine gene-phenotype associations from the literature. Our method achieved AUC values of 0.90 and 0.75 in recovering known gene-phenotype associations from HPO and MGI respectively. We posit that candidate genes and their relevant diseases should be expressed with similar phenotypes in publications. Thus, we demonstrate the utility of our approach by predicting disease candidate genes based on the semantic similarities of phenotypes associated with genes and diseases. To the best of our knowledge, this is the first study using an ontology based approach to extract gene-phenotype associations from the literature. We evaluated our disease candidate prediction model on the gene-disease associations from MGI. Our model achieved AUC values of 0.90 and 0.87 on OMIM (human) and MGI (mouse) datasets of gene-disease associations respectively. Our manual analysis on the text mined data revealed that our method can accurately extract gene-phenotype associations which are not currently covered by the existing public gene-phenotype resources. Overall, results indicate that our method can precisely extract known as well as new gene-phenotype associations from literature. All the data and methods are available at https://github.com/bio-ontology-research-group/genepheno.


A novel mutation in ferroportin implicated in iron overload.
Hereditary iron overload is associated with mutations in a number of genes involved in the regulation of iron metabolism. In this study we examined the molecular basis of iron overload in an individual from New Zealand and characterised the molecular and cellular defect. We analysed the ferroportin gene and a control population was screened using allele-specific PCR and denaturation analysis. Molecular characterisation was performed by immunofluorescence microscopy analysis of transfected cells. We analysed the ferritin levels of cells expressing wild-type and mutant ferroportin to define the nature of the molecular defect on iron transport. We identified a novel nucleotide substitution (c. 1014T>G) in the ferroportin gene leading to the S338R mutation. This mutation is not a common polymorphism. Cellular analysis of the mutant protein indicates that this amino acid change does not affect the localisation of the protein or its ability to transport iron. The S338R mutation results in a mutated ferroportin associated with iron overload and is predicted insensitive to regulation by the iron regulatory hormone hepcidin.


PirB regulates asymmetries in hippocampal circuitry.
Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.


From mechanisms to markers: novel noninvasive EEG proxy markers of the neural excitation and inhibition system in humans.
Brain function is a product of the balance between excitatory and inhibitory (E/I) brain activity. Variation in the regulation of this activity is thought to give rise to normal variation in human traits, and disruptions are thought to potentially underlie a spectrum of neuropsychiatric conditions (e.g., Autism, Schizophrenia, Downs' Syndrome, intellectual disability). Hypotheses related to E/I dysfunction have the potential to provide cross-diagnostic explanations and to combine genetic and neurological evidence that exists within and between psychiatric conditions. However, the hypothesis has been difficult to test because: (1) it lacks specificity-an E/I dysfunction could pertain to any level in the neural system- neurotransmitters, single neurons/receptors, local networks of neurons, or global brain balance - most researchers do not define the level at which they are examining E/I function; (2) We lack validated methods for assessing E/I function at any of these neural levels in humans. As a result, it has not been possible to reliably or robustly test the E/I hypothesis of psychiatric disorders in a large cohort or longitudinal patient studies. Currently available, in vivo markers of E/I in humans either carry significant risks (e.g., deep brain electrode recordings or using Positron Emission Tomography (PET) with radioactive tracers) and/or are highly restrictive (e.g., limited spatial extent for Transcranial Magnetic Stimulation (TMS) and Magnetic Resonance Spectroscopy (MRS). More recently, a range of novel Electroencephalography (EEG) features has been described, which could serve as proxy markers for E/I at a given level of inference. Thus, in this perspective review, we survey the theories and experimental evidence underlying 6 novel EEG markers and their biological underpinnings at a specific neural level. These cheap-to-record and scalable proxy markers may offer clinical utility for identifying subgroups within and between diagnostic categories, thus directing more tailored sub-grouping and, therefore, treatment strategies. However, we argue that studies in clinical populations are premature. To maximize the potential of prospective EEG markers, we first need to understand the link between underlying E/I mechanisms and measurement techniques.