bluuebunny/crossref_metadata_2025 huggingface dataset:
The long-term rapid increase in incidence of adenocarcinoma of the kidney in the USA, especially among younger ages
Authors: Zheng Tongzhang , Zhu Cairong , Bassig Bryan A , Liu Simin , Buka Stephen , Zhang Xichi , Truong Ashley , Oh Junhi , Fulton John , Dai Min , Li Ni , Shi Kunchong , Qian Zhengmin , Boyle Peter
Published: June 2019

Background

We previously observed a rapid increase in the incidence of renal cell carcinoma (RCC) in men and women between 1935 and 1989 in the USA, using data from the Connecticut Tumor Registry. This increase appeared to be largely explained by a positive cohort effect, but no population-based study has been conducted to comprehensively examine age-period-cohort effects by histologic types for the past decade.

Methods

We calculated age-adjusted and age-specific incidence rates of the two major kidney-cancer subtypes RCC and renal urothelial carcinoma, and conducted an age-period-cohort analysis of 114 138 incident cases of kidney cancer reported between 1992 and 2014 to the Surveillance, Epidemiology, and End Results programme.

Results

The age-adjusted incidence rates of RCC have been increasing consistently in the USA among both men and women (from 12.18/100 000 in 1992–1994 to 18.35/100 000 in 2010–2014 among men; from 5.77/100 000 in 1992–1994 to 8.63/100 000 in 2010–2014 among women). Incidence rates generally increased in successive birth cohorts, with a continuing increase in rates among the younger age groups (ages 0–54 years) in both men and women and among both Whites and Blacks. These observations were confirmed by age-period-cohort modelling, which suggested an increasing birth-cohort trend for RCC beginning with 1955 birth cohorts, regardless of the assumed value for the period effect for both men and women and for Whites and Blacks.

Conclusions

Known risk factors for kidney cancer may not fully account for the observed increasing rates or the birth-cohort pattern for RCC, prompting the need for additional etiologic hypotheses (such as environmental exposures) to investigate these descriptive patterns.
Studies of selective digestive decontamination as a natural experiment to evaluate topical antibiotic prophylaxis and cephalosporin use as population-level risk factors for enterococcal bacteraemia among ICU patients
Authors: Hurley James C
Published: June 2019

Background

Selective digestive decontamination (SDD) and selective oropharyngeal decontamination (SOD) regimens appear protective against ICU-acquired overall bacteraemia. These regimens can be factorized as topical antibiotic prophylaxis (TAP) with (SDD) or without (SOD) protocolized parenteral antibiotic prophylaxis (PPAP) using cephalosporins. Both TAP and cephalosporins are risk factors for enterococcal colonization although their impact on enterococcal bacteraemia within studies of SDD/SOD remains unclear.

Objectives

To benchmark the enterococcal bacteraemia incidence within component (control and intervention) groups of SDD/SOD studies among ICU patients versus studies without intervention (observational groups).

Methods

The literature was searched for SDD/SOD studies reporting enterococcal bacteraemia incidence data. In addition, component groups of studies of various non-antibiotic interventions served to provide additional points of reference.

Results

The mean incidence per 100 patients (and 95% CI) for enterococcal bacteraemia among 19 SDD/SOD studies was equally increased among concurrent control (2.1; 1.0%–4.7%) and intervention (2.3; 2.0%–2.7%) groups versus the benchmark incidence (0.8; 0.6%–1.2%) derived from 16 observational study groups and also versus 9 component groups from non-antibiotic studies. These higher incidences remained apparent (P < 0.02) in a meta-regression model adjusting for groupwide factors such as PPAP use, mechanical ventilation proportion, group mean length of stay >7 days and publication year.

Conclusions

The incidences of enterococcal bacteraemia within both concurrent control and intervention groups of SDD/SOD studies are unusually high compared with the literature-derived benchmark. The impact of parenteral cephalosporin used as PPAP additional to TAP on enterococcal bacteraemia incidence was indeterminate in this analysis.
The effective public enforcement of the prohibition of anti-competitive agreements: which factors influence the high percentage of annulments of Dutch cartel fines?
Authors: Outhuijse Annalies
Published: June 2019

The Dutch enforcement of the European and Dutch cartel prohibition is characterized by high rates of litigation and successful litigation. Several studies have devoted attention to these phenomena, all unraveling parts of the puzzle as to how the occurrence of these percentages can be explained. The subject of this article, an analysis of the factors which influence the rate of successful litigation, is however missing in this body of literature. To begin with, a theoretical framework of possible influencing factors is designed on the basis of relevant academic literature. In order to evaluate whether the factors identified in the literature can explain the Dutch practice, an assessment is carried out using several means, including a further analysis of the Dutch cartel practice, interviews with involved stakeholders, and comparisons with other Member States and Dutch market supervisors. The article concludes that specific factors that are woven into the Dutch practice (including specific court, party, and case characteristics), in combination with the nature of competition law, influence the Dutch annulment rate.
Assessment of the Capacity and Capability of Burn Centers to Respond to Burn Disasters in Belgium: A Mixed-Method Study
Authors: Al-Shamsi Mustafa , Moitinho de Almeida Maria , Nyanchoka Linda , Guha-Sapir Debarati , Jennes Serge
Published: June 2019

Burn disaster is defined as a massive influx of patients that exceeds a burn center’s capacity and capability. This study investigates the capacity and capability of burn centers to respond to burn disasters in the Belgian ground. Quantitative survey and qualitative semistructured interview questionnaires were administered directly to key informants of burn centers. The data collected from both methods were compared to get a more in-depth overview of the issue. Quantitative data were converted into a narrative to enrich the qualitative data and included in the thematic analysis. Finally, data from both methods were analyzed and organized into five themes. The Belgian Association of Burn Injury (BABI) has a specific prehospital plan for burn disaster management. Once the BABI Plan is activated, all burn centers respond as one entity. Burn Team (B-Team) is a professional team that is formed in case of urgent need and it is deployed to a scene or to nonburn specialized hospitals to help in disaster relief. The challenges for burn disasters response occur particularly in the area of triage, transfer, communication, funding, and training. We conclude that there is a variation in the capacity and capability of burn centers. Overall, the system of burn disaster management is advanced and it is comparable to other high-income countries. Nevertheless, further improvement in the areas of preparation, triage, communication, and finally training would make disaster response more resilient in the future. Therefore, there is still space for further improvement of the management of burn disasters in Belgium.
Historical demography of the Caribbean spiny lobster Panulirus argus (Latreille, 1804) (Decapoda: Achelata: Palinuridae) in the Florida Keys, USA inferred using single nucleotide polymorphisms (SNPs)
Authors: Baeza J Antonio , Umaña-Castro Rodolfo , Mejia-Ortiz Luis M
Published: June 2019

The Caribbean spiny lobster Panulirus argus (Latreille, 1804) is an important species in shallow-water coral reefs and target of the most lucrative fishery in the Caribbean Sea. We explored historical demography in P. argus inferred using single nucleotide polymorphisms (SNPs). We expected an increase in population size of P. argus from Florida, USA starting ~18,000–24,000 years ago, after the Last Glacial Maximum, when ice sheets started to retreat and sub-tropical/tropical shallow coastal waters warmed up. A total of 10 lobsters were collected from shallow reefs in the Florida Keys, Florida, USA. One microgram of gDNA extracted from each specimen was used for RAD library construction using established protocols. A panel of 1643 SNPs obtained after interrogation of RAD-tags was used to calculate a site frequency spectrum (SFS). The observed SFS for the Florida population of P. argus exhibited a non-normal distribution peaking at singleton SNPs. The expected SFS in a total of six different candidate demographic models with dissimilar population size changes through time (i.e., standard neutral, exponential growth, bottleneck, bottleneck + growth, two epochs, and three epochs) were numerically computed in the software ∂a∂i and a model selection approach was implemented to test which expected model(s) best fitted the empirical SFS. The model selection approach indicated that the bottleneck + growth model most closely matched the observed SFS; P. argus experienced a population decline at about 1.9 (0.75–5.7) mya, to then recover and growth exponentially until present time. In disagreement with expectations, population expansion started much earlier than ~18,000–24,000 years ago. Fisheries and conservation studies are expected to profit from the evaluation of genomic and population variability in this species using demographic models, as shown here. Studies exploring population connectivity and locality-specific demographic history of P. argus are underway.
Three-level distributed analysis for transmission performance of deep-sea electromagnetic inductive coupling temperature-salinity-depth chain
Authors: Zheng Yu , Qin Xiaocong , Li Hongzhi , Zhang Xiaowei , Zhang Sai
Published: June 2019

Inductive coupling temperature-salinity-depth chain is an important instrument for measuring the deep-sea environment. Using the electromagnetic induction principle, the bidirectional data transmission from the overwater control equipment to an underwater sensor can be realized. However, due to attenuation in marine environments, it is difficult to realize a long distance and efficient transmission. In order to accurately analyze the channel transmission characteristics of an inductive coupling temperature-salinity-depth chain, a three-level distributed prototype of the transmission channel using COMSOL Multiphysics is constructed. The transmission characteristics of the channel are analyzed at various depths. The analysis of a three-level simulation model demonstrates that the seawater resistivity is relatively stable, independent of detection depth. When the transmission frequency is 10 kHz and the length of the cable is 60 m, the transmission efficiency of the single node transmission channel is 2.9%. Moreover, the transmission efficiency is reduced to 2.6%, when the sensor nodes in the transmission channel are 10, while it may be less than 1% with the decrease of the inductance. The seawater resistivity and the inductance of magnetic ring significantly influence the performance of transmission channel. Optimizing the inductance of the magnetic ring and improving the frequency of the transmission signal are extremely important for the improvement of the transmission performance of an electromagnetic inductive coupling temperature-salinity-depth chain.
Single incision laparoscopic surgery (SILS) for Meckel’s diverticulum
Authors: Kuramoto Kunitaka , Nakahara Osamu , Maeda Yuto , Kumamoto Sayahito , Tsuji Akira , Hayashida Shintaro , Oya Yuki , Shibata Hidekatsu , Iizaka Masayoshi , Tomiyasu Shinjiro , Hayashi Hironori , Inomata Yukihiro , Baba Hideo
Published: June 2019

A 65-year-old male patient presented with a chief complaint of abdominal pain. Abdominal computed tomography (CT) showed slight intestinal dilation and obstruction of the upper right quadrant of the small intestine, while ectopic gastric mucosal scintigraphy revealed abnormal accumulation in agreement with the CT-identified structure. The cause of bowel obstruction was diagnosed as Meckel’s diverticulum; the patient was referred for surgery. A small laparotomy was performed with a 35-mm skin incision to the center of the navel. Once a lap disk was attached, a laparoscope was inserted to visualize the abdominal cavity. The small intestine that includes the structure was pulled out from the umbilicus to the outside of the peritoneal cavity and partially resected. On the pathological tissue findings, the patient was diagnosed with Meckel’s diverticulum. We report our experience with single-lap laparoscopic surgery for a case of intestinal obstruction caused by Meckel’s diverticulum and review pertinent literature.
Digital humanities in Sweden and its infrastructure: Status quo and the sine qua non
Authors: Golub Koraljka , Göransson Elisabet , Foka Anna , Huvila Isto
Published: June 2019

The article offers a state-of-the-art overview of a number of Digital Humanities (DH) initiatives that have emerged in Sweden over the past decade. We identify two major developments that seem to be taking place within DH, with a specific focus on the infrastructural aspects of the development: (1) a strive to open up and broaden the research output and (2) multi-disciplinary collaboration and its effects. The two major components accentuate the new infrastructural patterns that are developing and the challenges these infer on universities. While current research is at large multi-disciplinary, developing infrastructures also enable the move towards post-disciplinarity, bringing the universities closer to the surrounding society. At five universities in Sweden, individual-sited infrastructures supporting DH research have been built today. They are complemented by national and international infrastructures, thus supporting developments and tackling some of the major challenges. In the article, the relations between individual disciplines, the question of multi- and post-disciplinarity, and the field of Digital Humanities are discussed, while stressing the factors necessary—sine qua non—for a fruitful development of the scholarly infrastructures.
The role of Trp53 in the mouse embryonic response to DNA damage
Authors: Wilson Yvonne , Morris Ian D , Kimber Susan J , Brison Daniel R
Published: June 2019

Apoptosis occurs primarily in the blastocyst inner cell mass, cells of which go on to form the foetus. Apoptosis is likely to play a role in ensuring the genetic integrity of the foetus, yet little is known about its regulation. In this study, the role of the mouse gene, transformation-related protein 53 (Trp53) in the response of embryos to in vitro culture and environmentally induced DNA damage was investigated using embryos from a Trp53 knockout mouse model. In vivo-derived blastocysts were compared to control embryos X-irradiated at the two-cell stage and cultured to Day 5. An analysis of DNA by comet assay demonstrated that 1.5 Gy X-irradiation directly induced damage in cultured two-cell mouse embryos; this was correlated with retarded development to blastocyst stage and increased apoptosis at the blastocyst stage but not prior to this. Trp53 null embryos developed to blastocysts at a higher frequency and with higher cell numbers than wild-type embryos. Trp53 also mediates apoptosis in conditions of low levels of DNA damage, in vivo or in vitro in the absence of irradiation. However, following DNA damage induced by X-irradiation, apoptosis is induced by Trp53 independent as well as dependent mechanisms. These data suggest that Trp53 and apoptosis play important roles in normal mouse embryonic development both in vitro and in vivo and in response to DNA damage. Therefore, clinical ART practices that alter apoptosis in human embryos and/or select embryos for transfer, which potentially lack a functional Trp53 gene, need to be carefully considered.
Comparison of Adverse Drug Reactions Between Patients Treated With Ceftaroline or Ceftriaxone: A Single-Center, Matched Cohort Study
Authors: Jansen Jeffrey W , Linneman Travis W , Tan Xing , Moenster Ryan P
Published: June 2019

Background

Little information is available on the relative tolerability of ceftaroline versus other cephalosporins in clinical practice. We sought to compare adverse drug reactions (ADRs) associated with ceftaroline with those associated with ceftriaxone in hospitalized patients.

Materials and Methods

This was a retrospective, single-center matched cohort (according to age, indication, and duration) study of patients treated with ceftaroline or ceftriaxone at the VA St Louis Health Care System between 29 October 2010 and 28 March 2017, to compare rates of ADRs between the agents. Patients included received ≥2 doses of either medication to treat osteomyelitis, acute bacterial skin and skin structure infection, blood stream infection, pneumonia, infective endocarditis, septic arthritis, prosthetic joint infection, or empyema. The primary and secondary outcomes were the composite of any ADR during therapy and any ADR leading to premature discontinuation of therapy. The ADRs evaluated included rash, neutropenia, acute kidney injury, eosinophilia, thrombocytopenia, transaminitis, and hyperbilirubinemia.

Results

After matching, 50 patients per group were included and analyzed. An ADR occurred in 20% (10 of 50) of patients treated with ceftriaxone and 16% (8 of 50) of those treated with ceftaroline (P = .60). Two percent (1 of 50) of those treated with ceftriaxone and 16% (8 of 50) treated with ceftaroline had therapy discontinued owing to an ADR (P = .03). The most common ADR was eosinophilia (3 of 50) in the ceftriaxone group and rash (5 of 50) in the ceftaroline group. Ceftaroline therapy was identified as an independent risk factor for an ADR requiring premature discontinuation (odds ratio, 10.2; 95% confidence interval, 1.19–87.8; P = .03).

Conclusions

Although there was no difference in the rates of ADRs between patients in the ceftriaxone and ceftaroline groups, significantly more ceftaroline-treated patients required premature discontinuation.
Identifying Schizo-Obsessive Comorbidity by Tract-Based Spatial Statistics and Probabilistic Tractography
Authors: Wang Yong-ming , Yang Zhuo-ya , Cai Xin-lu , Zhou Han-yu , Zhang Rui-ting , Yang Han-xue , Liang Yun-si , Zhu Xiong-zhao , Madsen Kristoffer Hougaard , Sørensen Thomas Alrik , Møller Arne , Wang Zhen , Cheung Eric F C , Chan Raymond C K
Published: June 2019

A phenomenon in schizophrenia patients that deserves attention is the high comorbidity rate with obsessive-compulsive disorder (OCD). Little is known about the neurobiological basis of schizo-obsessive comorbidity (SOC). We aimed to investigate whether specific changes in white matter exist in patients with SOC and the relationship between such abnormalities and clinical parameters. Twenty-eight patients with SOC, 28 schizophrenia patients, 30 OCD patients, and 30 demographically matched healthy controls were recruited. Using Tract-based Spatial Statistics and Probabilistic Tractography, we examined the pattern of white matter abnormalities in these participants. We also used ANOVA and Support Vector Classification of various white matter indices and structural connection probability to further examine white matter changes among the 4 groups. We found that patients with SOC had decreased fractional anisotropy (FA) and increased radial diffusivity in the right sagittal stratum and the left crescent of the fornix/stria terminalis compared with healthy controls. We also found changed connection probability in the Default Mode Network, the Subcortical Network, the Attention Network, the Task Control Network, the Visual Network, the Somatosensory Network, and the cerebellum in the SOC group compared with the other 3 groups. The classification results further revealed that FA features could differentiate the SOC group from the other 3 groups with an accuracy of .78. These findings highlight the specific white matter abnormalities found in patients with SOC.
A Call to Accountability: Reporting Outcomes in Vascularized Composite Allotransplantation
Authors: Benedict James L. , Robbins Nicholas L. , Kaplan Bruce , Breidenbach Warren C.
Published: June 2019

Because nearly all the vascularized composite allotransplants performed in the United States have been proposed and carried out as research, the ethical duty to report outcomes pertains. This duty is set forth in several international statements, including the World Health Organization’s Statement on Public Disclosure of Clinical Trial Results, the 2013 Helsinki Declaration, and the Singapore Statement on Research Integrity. These international statements call for the reporting of negative and inconclusive outcomes as well as positive outcomes, and for the reporting of results from previously unreported past research. In 2014, the Organ Procurement and Transplant Network vascularized composite allotransplant committee proposed mandatory data collection and submission requirements for transplants, but only for those which took place in September 2015 or later. Reporting of data for the allotransplants which took place before September 2015 was regarded as optional, even though the pre-September 2015 transplants represent the majority of vascularized composite allotransplants in the United States and all the long-term outcome data. We encourage the American Society of Reconstructive Transplantation and the Organ Procurement and Transplant Network committee to embrace the international ethical standards and to hold all vascularized composite allotransplant programs in the United States accountable for reporting data on outcomes of pre-September 2015 transplants.
Reduction Mammaplasty: What Cup Size Will I Be?
Authors: Chan Marion , Lonie Sarah , Mackay Sean , MacGill Kirstie
Published: June 2019

Background:

Predicting cup size after reduction mammaplasty is a challenge well recognized by plastic surgeons. This study presents a method whereby the weight of tissue to be excised can be predicted on the basis of the initial and desired cup size.

Methods:

Breast density was calculated from resection specimens. Cup volumes of a specific range of bra style were then measured by filling the bra cups with modeling clay on a mannequin and the volume measured via water displacement. These data were then correlated to breast tissue volume and weight.

Results:

The average breast tissue density calculated was 0.98 g/ml (SD = 0.05). Bra cup volume measurements showed a steady progression according to both cup and band sizes. A table was constructed to predict the weight of tissue required for excision to achieve the desired change in cup size.

Conclusion:

These results can assist plastic surgeons in predicting the amount of breast tissue to excise to achieve a given cup size. A secondary use of these results is a breast volume guide for implant planning.
Non-narcotic Perioperative Pain Management in Prosthetic Breast Reconstruction During an Opioid Crisis: A Systematic Review of Paravertebral Blocks
Authors: Tokita Hanae K. , Polanco Thais O. , Shamsunder Meghana G. , Dabic Stefan , Patel Vaidehi G. , Allen Robert J , Dayan Joseph H. , Mehrara Babak J. , Matros Evan , Nelson Jonas A.
Published: June 2019

Background:

Alternatives to postoperative, narcotic pain management following implant-based, postmastectomy breast reconstruction (IBR) must be a focus for plastic surgeons and anesthesiologists, especially with the current opioid epidemic. Paravertebral blocks (PVBs) are a regional technique that has demonstrated efficacy in patients undergoing a variety of breast cancer–related surgeries. However, a specific understanding of PVB’s efficacy in pain management in patients who undergo IBR is lacking.

Methods:

A systematic search of PubMed, EMBASE, and Cochrane Library electronic database was conducted to examine PVB administration in mastectomy patients undergoing IBR. Data were abstracted regarding: authors, publication year, study design, patient demographics, tumor laterality, tumor stage, type, and timing of reconstruction. The primary outcome was PVB efficacy, represented as patient-reported pain scores. Secondary outcomes of interest include narcotic consumption, postoperative nausea and vomiting, antiemetic use, and length of stay.

Results:

The search resulted in 1,516 unique articles. After title and abstract screening, 29 articles met the inclusion criteria for full-text review. Only 7 studies were included. Of those, 2 studies were randomized control trials and 5 were retrospective cohort studies. Heterogeneity of included studies precluded a meta-analysis. Overall, PVB patients had improved pain control, and less opioid consumption.

Conclusion:

PVBs are a regional anesthesia technique which may aid in pain management in the breast reconstructive setting. Evidence suggests that PVBs aid in controlling acute postoperative pain, reduce opioid consumption, and improve patient length of stay. However, some conflicting findings demonstrate a need for continued research in this area of pain control.
Shot Noise Explains the Petkau 22Na+ Result for Rupture of a Model Phospholipid Membrane
Authors: Datesman Aaron M.
Published: June 2019

The action of free radicals is believed responsible for much or most biological injury resulting from exposure to ionizing radiation. These molecules in solution possess short lifetimes on the order of nanoseconds to microseconds. As a result, the dose—which measures the energy dissipated in tissue due to radiolysis—should not be considered a reliable indicator of the free radical concentration, nor of the chemical effects that follow from it. Rather, the chemical state of affected tissue is properly represented only by the dissipated power, which describes the distribution of energy with time. The present report demonstrates the validity of this assertion using data contained in a report describing a benchtop experiment published in 1972. The experiment used the visible rupture of a model phospholipid membrane as a means to quantify the degree of chemical insult caused by ionizing radiation. The experiment found that beta doses in the range from 1–10 rad were equivalent to x-ray rupture doses of 3,500 rad. This report demonstrates that the experimental results are convincingly explained by reference to the properly calculated time-averaged dissipated power due to beta decay. The theoretical explanation is derived by analogy to a well-understood result from electronic systems known as shot noise. If the result described in this report is demonstrated to extrapolate from the benchtop to living systems, then it is likely that exposure to beta radiation via internal incorporation is far more hazardous than commonly believed. The finding could be revolutionary in the field of health physics.
Two-Year Incidence and Associated Factors of Dry Eye Among Residents in Shanghai Communities With Type 2 Diabetes Mellitus
Authors: Huang Xiaobo , Zhang Pei , Zou Xinrong , Xu Yi , Zhu Jianfeng , He Jiangnan , Zhang Bo , Lu Lina , Zou Haidong
Published: June 2019

Objective:

To evaluate the 2-year incidence and associated factors of dry eye (DE) among community residents with type 2 diabetes mellitus (DM).

Methods:

For confirmed type 2 DM residents in the Xinjing community of Shanghai in China, 2 surveys on DE and related factors were performed in 2016 and 2018. The survey content included general information, subjective symptom questionnaires, tear-film break-up time test, Schirmer I test, corneal fluorescence staining (FL), slit-lamp examination, and examination of blood and urine samples. Symptoms of depression were evaluated using the Center for Epidemiologic Studies Depression (CES-D) scale. Dry eye was diagnosed based on the diagnostic standards developed by the Asia Dry Eye Society in 2016.

Results:

The 2-year incidence of DE among 460 type 2 DM residents was 33.7% (95% confidence interval [CI]=29.6%–38.3%). The incidence of DE significantly increased with increasing age (P<0.01). The incidence among women (35.7%) was not statistically significant compared with that of men (31.0%). In the multivariate logistic regression model, age (odds ratio [OR]=1.03, 95% CI=1.01–1.06, P=0.04), corneal sensitivity (OR=0.97, 95% CI=0.94–0.99, P=0.03), and depressive symptom score (OR=1.04, 95% CI = 1.00–1.08, P=0.04) were associated factors for the incidence of DE. In the CES-D scale, two items, “I felt that everything I did was an effort” and “I felt sad,” were significantly correlated with DE onset.

Conclusion:

The incidence of DE among community residents with type 2 DM was high. Screening for DE among DM residents, especially residents with advanced age, corneal hypoesthesia, and depression, should be strengthened.
Prevalence and Associations of Myopic Anisometropia in Chinese Adults
Authors: Wang Xianglong , Pan Jian , Zhang Yang , Lan Yuan , Zuo Jingjing , Jiang Zipei
Published: June 2019

Purpose:

To investigate the prevalence and associations of myopic anisometropia in Chinese adults.

Methods:

A total of 3,791 Chinese refractive surgery candidates with myopia (25.15±7.09 years old, Mean±SD) were recruited. All eyes underwent a standardized ophthalmological examination. Associations between myopic anisometropia and age, gender, spherical ametropia, astigmatism, and axial length (AL) were analyzed by means of the chi-squared test, nonparametric Kruskal–Wallis or Mann–Whitney test, binomial logistic regression analyses, and multivariate logistic regression analysis.

Results:

The mean myopic anisometropic level was 0.96 D and prevalence of myopic anisometropia was 29.62% (defined as myopic anisometropia ≥1.00 D). The prevalence and severity of myopic anisometropia increased with age, larger interocular AL difference, and higher cylindrical power (all P<0.001). Myopic anisometropia showed a U-shaped correlation with spherical equivalent (SE) refractive error and V-shaped correlations with AL, J0 and J45. Myopic anisometropia was most strongly associated with interocular AL difference (P<0.001).

Conclusions:

Compared with previous reports, this study revealed an even higher prevalence of myopic anisometropia and showed a U-shaped correlation with SE and a V-shaped correlation with AL. These results indicate that the formation of myopic anisometropia could be related to neural control in the binocular AL growth balance. Further study is needed to clarify this presumption.
Hormonal Dynamics Effect of Serum Insulin-Like Growth Factor I and Cortisol/Dehydroepiandrosterone Sulfate Ratio on Symptom Severity of Major Depressive Disorder
Authors: Tajiri Misuzu , Suzuki Yutaro , Tsuneyama Nobuto , Arinami Hiroshi , Someya Toshiyuki
Published: June 2019

Background

Insulin-like growth factor I (IGF-I) is a neurotrophic factor produced by the hypothalamic-pituitary-somatotropic axis and is considered a potential contributor to the pathology of major depressive disorder (MDD). Although it is known that the hypothalamic-pituitary-adrenal axis and cortisol are involved in the pathology of MDD, the association with dehydroepiandrosterone sulfate (DHEAS) remains unclear. The current study sought to clarify the relationship between these hormones and the pathology of MDD.

Methods

Subjects were 91 Japanese patients with a diagnosis of MDD. Serum IGF-I, cortisol, and DHEAS were measured. Samples were taken before breakfast after overnight fasting. Depressive symptoms were assessed using the Hamilton Rating Scale for Depression (HAM-D).

Results

Subjects included 59 men and 32 women with an average age of 44.1 ± 13.1 years (mean ± SD). The blood IGF-I level was 152.0 ± 50.0 ng/mL, the cortisol level was 10.1 ± 4.6, and the DHEAS level was 201.3 ± 112.7 μg/dL. The mean HAM-D score was 13.9 ± 9.0. Serum IGF-I levels were not correlated with cortisol. Higher IGF-I, cortisol, and cortisol/DHEAS ratios were associated with higher HAM-D scores (adjusted R
2 = 0.240, P < 0.001), and higher IGF-I and cortisol were associated with higher melancholic or suicide subscores (adjusted R
2 = 0.200, P < 0.001; adjusted R
2 = 0.273, P < 0.001).

Conclusions

Our findings suggest that hormonal dysregulation of the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-somatotropic axes may be related to the symptom severity of MDD, melancholia, and suicide-related factors.
Should We Assess Vitamin D Status in Pediatric Patients With Celiac Disease?
Authors: Ahlawat Rajni , Weinstein Toba , Markowitz James , Kohn Nina , Pettei Michael J
Published: June 2019

Objectives:

Screening for vitamin D status in celiac disease (CD) has been recommended but the literature provides varying support. We sought to assess the vitamin D status in newly diagnosed children with CD and in a non‐CD control population and relate them to vitamin D intake.

Methods:

In a cross‐sectional study, serum 25‐hydroxyvitamin D (25‐OHD) levels were drawn in children with newly diagnosed CD and compared with pediatric outpatients with functional abdominal complaints. Anthropometric data as well as vitamin D intake based on milk and multivitamin ingestion were collected.

Results:

Thirty‐eight newly diagnosed CD patients (10.4 ± 3.0 years old; 50% girls) and 82 controls (11.2 ± 4.2 years old; 58.5% girls) were studied. Both groups were similar except for average daily D intake and BMI. There was no statistical difference in mean 25‐OHD levels between CD (26.4 ± 8.0 ng/mL) and controls (23.5 ± 8.2 ng/mL) [P ≤ 0.07]. Both groups had high percentages of suboptimal D status (65.8% CD and 79.3% controls). 25‐OHD levels significantly correlated with age (r = −0.262; P < 0.0038) and estimated vitamin D intake (r = 0.361; P < 0.0001).

Conclusions:

No significant difference in 25‐OHD levels was noted between newly diagnosed CD and controls, but inadequate 25‐OHD levels were common in both. 25‐OHD levels were highly associated with vitamin D intake demonstrating similar vitamin D absorption between patients and controls. As CD is associated with bone disease and D status is frequently low, efforts at optimizing D, such as screening levels at diagnosis need to be conducted.
NanoVar: Accurate Characterization of Patients’ Genomic Structural Variants Using Low-Depth Nanopore Sequencing
Authors: Tham Cheng Yong , Tirado-Magallanes Roberto , Goh Yufen , Fullwood Melissa J. , Koh Bryan T.H. , Wang Wilson , Ng Chin Hin , Chng Wee Joo , Thiery Alexandre , Tenen Daniel G. , Benoukraf Touati
Published: June 2019

Despite the increasing relevance of structural variants (SV) in the development of many human diseases, progress in novel pathological SV discovery remains impeded, partly due to the challenges of accurate and routine SV characterization in patients. The recent advent of third-generation sequencing (3GS) technologies brings promise for better characterization of genomic aberrations by virtue of having longer reads. However, the applications of 3GS are restricted by their high sequencing error rates and low sequencing throughput. To overcome these limitations, we present NanoVar, an accurate, rapid and low-depth (4X) 3GS SV caller utilizing long-reads generated by Oxford Nanopore Technologies. NanoVar employs split-reads and hard-clipped reads for SV detection and utilizes a neural network classifier for true SV enrichment. In simulated data, NanoVar demonstrated the highest SV detection accuracy (F1 score = 0.91) amongst other long-read SV callers using 12 gigabases (4X) of sequencing data. In patient samples, besides the detection of genomic aberrations, NanoVar also uncovered many normal alternative sequences or alleles which were present in healthy individuals. The low sequencing depth requirements of NanoVar enable the use of Nanopore sequencing for accurate SV characterization at a lower sequencing cost, an approach compatible with clinical studies and large-scale SV-association research.
3D observation of large-scale subcellular dynamics in vivo at the millisecond scale
Authors: Wu Jiamin , Lu Zhi , Qiao Hui , Zhang Xu , Zhanghao Karl , Xie Hao , Yan Tao , Zhang Guoxun , Li Xiaoxu , Jiang Zheng , Lin Xing , Fang Lu , Zhou Bing , Fan Jingtao , Xi Peng , Dai Qionghai
Published: June 2019

Observing large-scale three-dimensional (3D) subcellular dynamics in vivo at high spatiotemporal resolution has long been a pursuit for biology. However, both the signal-to-noise ratio and resolution degradation in multicellular organisms pose great challenges. Here, we propose a method, termed Digital Adaptive Optics Scanning Lightfield Mutual Iterative Tomography (DAOSLIMIT), featuring both 3D incoherent synthetic aperture and tiled wavefront correction in post-processing. We achieve aberration-free fluorescence imaging in vivo over a 150 × 150 × 16 μm3 field-of-view with the spatiotemporal resolution up to 250 nm laterally and 320 nm axially at 100 Hz, corresponding to a huge data throughput of over 15 Giga-voxels per second. Various fast subcellular processes are observed, including mitochondrial dynamics in cultured neurons, membrane dynamics in zebrafish embryos, and calcium propagation in cardiac cells, human cerebral organoids, and Drosophila larval neurons, enabling simultaneous in vivo studies of morphological and functional dynamics in 3D.
MetaCurator: A hidden Markov model-based toolkit for extracting and curating sequences from taxonomically-informative genetic markers
Authors: Richardson Rodney T. , Sponsler Douglas B. , McMinn-Sauder Harper , Johnson Reed M.
Published: June 2019

The community-level analysis of samples containing diverse genetic material, via metabarcoding and metagenomic approaches, is increasingly popular. While the production of sequence data for such studies has become straightforward, questions remain about how best to analyze and taxonomically characterize sequence data. For many sequence classification approaches, an important component of the workflow involves the curation of reference sequences. Ideally, this involves trimming away extraneous sequence at the 3 prime and 5 prime ends of the target marker of interest, as well as the removal of reference sequence duplicates. Here, we present MetaCurator, a software package written in Python, designed for automated reference sequence curation and highly generalizable across markers and study systems. MetaCurator is organized in a modular fashion, so users can implement tools individually in addition to utilizing the automated and flexible MetaCurator parental code. Aside from modules used to organize and format taxonomic lineage data, MetaCurator contains two signature tools. IterRazor utilizes profile hidden Markov models and an iterative search framework to exhaustively identify and extract the precise amplicon marker of interest from available reference sequence data. DerepByTaxonomy then facilitates sequence dereplication using a taxonomically aware approach, removing duplicates only when they belong to the same taxon. This is important for cases of incomplete lineage sorting between species and for highly conserved markers, such as plantrbcLandtrnL, which often display no sequence divergence across taxa, even at the genus level.

Availability and implementation

MetaCurator is supported on OSX and Linux (RedHat/CentOS) and is freely available under a GPL v3.0 license athttps://github.com/RTRichar/MetaCurator.

Contact

rtr87@yorku.ca

Supplemental information

Code associated with this work is available athttps://github.com/RTRichar/MetabarcodeDBsV2and additional analysis is presented in supplementary files.
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced TF binding
Authors: Srivastava Divyanshi , Aydin Begüm , Mazzoni Esteban O. , Mahony Shaun
Published: June 2019

Transcription factor (TF) binding specificity is determined via a complex interplay between the TF’s DNA binding preference and cell type-specific chromatin environments. The chromatin features that correlate with TF binding in a given cell type have been well characterized. For instance, the binding sites for a majority of TFs display concurrent chromatin accessibility. However, concurrent chromatin features reflect the binding activities of the TF itself, and thus provide limited insight into how genome-wide TF-DNA binding patterns became established in the first place. To understand the determinants of TF binding specificity, we therefore need to examine how newly activated TFs interact with sequence and preexisting chromatin landscapes.

Here, we investigate the sequence and preexisting chromatin predictors of TF-DNA binding by examining the genome-wide occupancy of TFs that have been induced in well-characterized chromatin environments. We develop Bichrom, a bimodal neural network that jointly models sequence and preexisting chromatin data to interpret the genome-wide binding patterns of induced TFs. We find that the preexisting chromatin landscape is a differential global predictor of TF-DNA binding; incorporating preexisting chromatin features improves our ability to explain the binding specificity of some TFs substantially, but not others. Furthermore, by analyzing site-level predictors, we show that TF binding in previously inaccessible chromatin tends to correspond to the presence of more favorable cognate DNA sequences. Bichrom thus provides a framework for modeling, interpreting, and visualizing the joint sequence and chromatin landscapes that determine TF-DNA binding dynamics.
Towards an Objective Evaluation of EEG/MEG Source Estimation Methods: The Linear Tool Kit
Authors: Hauk Olaf , Stenroos Matti , Treder Matthias
Published: June 2019

The question “What is the spatial resolution of EEG/MEG?” can only be answered with many ifs and buts, as the answer depends on a large number of parameters. Here, we describe a framework for resolution analysis of EEG/MEG source estimation, focusing on linear methods. The spatial resolution of linear methods can be evaluated using the resolution matrix, which contains the point-spread and cross-talk functions (PSFs and CTFs), respectively. Both of them have to be taken into account for a full characterization of spatial resolution. They can be used to compute a range of quantitative resolution metrics, which should cover at the last three aspects of those functions: localization accuracy, spatial extent, and relative amplitude. Here, we first provide a tutorial-style introduction to resolution analysis of linear source estimation methods. We then apply these concepts to evaluate the benefit of combining EEG and MEG measurements, and to compare weighted and normalized L2-minimum-norm estimation and spatial filters. We confirm and extend previous results, showing that adding EEG to MEG improves spatial resolution, and that different methods offer different compromises among different resolution criteria. We hope that our approach will help EEG/MEG researchers in the interpretation of source estimation results, the design of new experiments, and the development of new MEG systems.
On set-based association tests: insights from a regression using summary statistics
Authors: Zhao Yanyan , Sun Lei
Published: June 2019

Motivated by, but not limited to, association analyses of multiple genetic variants, we propose here a summary statistics-based regression framework. The proposed method requires only variant-specific summary statistics, and it unifies earlier methods based on individual-level data as special cases. The resulting score test statistic, derived from a linear mixed-effect regression model, inherently transforms the variant-specific statistics using the precision matrix to improve power for detecting sparse alternatives. Furthermore, the proposed method can incorporate additional variant-specific information with ease, facilitating omic-data integration. We study the asymptotic properties of the proposed tests under the null and alternatives, and we investigate efficient p-value calculation in finite samples. Finally, we provide supporting empirical evidence from extensive simulation studies and two applications.
High Throughput Evolution of Near Infrared Serotonin Nanosensors
Authors: Jeong Sanghwa , Yang Darwin , Beyene Abraham G. , Gest Anneliese M.M. , Landry Markita P.
Published: June 2019

Release and reuptake of neuromodulator serotonin, 5-HT, is central to mood regulation and neuropsychiatric disorders, whereby imaging serotonin is of fundamental importance to study the brain’s serotonin signaling system. We introduce a reversible near-infrared nanosensor for serotonin (nIRHT), for which synthetic molecular recognition toward serotonin is systematically evolved from ssDNA-carbon nanotube constructs generated from large libraries of 6.9 × 1010unique ssDNA sequences. nIRHT produces a ∼200% fluorescence enhancement upon exposure to serotonin with a Kd= 6.3 µM affinity. nIRHT shows selective responsivity towards serotonin over serotonin analogs, metabolites, and receptor-targeting drugs, and a 5-fold increased affinity for serotonin over dopamine. Further, nIRHT can be introduced into the brain extracellular space in acute slice, and can be used to image exogenous serotonin reversibly. Our results suggest evolution of nanosensors could be generically implemented to rapidly develop other neuromodulator probes, and that these probes can image neuromodulator dynamics at spatiotemporal scales compatible with endogenous neuromodulation.
Cell volume distributions in exponentially growing populations
Authors: Bokes Pavol , Singh Abhyudai
Published: June 2019

Stochastic effects in cell growth and division drive variability in cellular volumes both at the single-cell level and at the level of growing cell populations. Here we consider a simple and tractable model in which cell volumes grow exponentially, cell division is symmetric, and its rate is volume-dependent. Consistently with previous observations, the model is shown to sustain oscillatory behaviour with alternating phases of slow and fast growth. Exact simulation algorithms and large-time asymptotics are developed and cross-validated for the single-cell and whole-population formulations of the model. The two formulations are shown to provide similar results during the phases of slow growth, but differ during the fast-growth phases. Specifically, the single-cell formulation systematically underestimates the proportion of small cells. More generally, our results suggest that measurable characteristics of cells may follow different distributions depending on whether a single-cell lineage or an entire population is considered.