bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterizing beach intertidal bar systems using multi‐annual LiDAR data
Authors: Miles Andrew , Ilic Suzana , Whyatt Duncan , James Mike R.
Published: February 2019

Intertidal bars are common in mesotidal/macrotidal low‐to‐moderate energy coastal environments and an understanding of their morphodynamics is important from the perspective of both coastal scientists and managers. However, previous studies have typically been limited by considering bar systems two‐dimensionally, or with very limited alongshore resolution. This article presents the first multi‐annual study of intertidal alongshore bars and troughs in a macrotidal environment using airborne LiDAR (light detection and ranging) data to extract three‐dimensional (3D) bar morphology at high resolution.

Bar and trough positions are mapped along a 17.5 km stretch of coastline in the northwest of England on the eastern Irish Sea, using eight complete, and one partial, LiDAR surveys spanning 17 years. Typically, 3–4 bars are present, with significant obliquity identified in their orientation. This orientation mirrors the alignment of waves from the dominant south‐westerly direction of wave approach, undergoing refraction as they approach the shoreline. Bars also become narrower and steeper as they migrate onshore, in a pattern reminiscent of wave shoaling. This suggests that the configuration of the bars is being influenced by overlying wave activity. Net onshore migration is present for the entire coastline, though rates vary alongshore, and periods of offshore migration may occur locally, with greatest variability between northern and southern regions of the coastline.

This work highlights the need to consider intertidal bar systems as 3D, particularly on coastlines with complex configurations and bathymetry, as localized studies of bar migration can overlook 3D behaviour. Furthermore, the wider potential of LiDAR data in enabling high‐resolution morphodynamic studies is clear, both within the coastal domain and beyond. © 2019 John Wiley & Sons, Ltd.
Intermittent demand forecasting in the Enterprise: Empirical verification
Authors: Doszyń Mariusz
Published: February 2019

Forecasting methods are often valued by means of simulation studies. For intermittent demand items there are often very few non–zero observations, so it is hard to check any assumptions, because statistical information is often too weak to determine, for example, distribution of a variable. Therefore, it seems important to verify the forecasting methods on the basis of real data. The main aim of the article is an empirical verification of several forecasting methods applicable in case of intermittent demand. Some items are sold only in specific subperiods (in given month in each year, for example), but most forecasting methods (such as Croston's method) give non–zero forecasts for all periods. For example, summer work clothes should have non–zero forecasts only for summer months and many methods will usually provide non–zero forecasts for all months under consideration. This was the motivation for proposing and testing a new forecasting technique which can be applicable to seasonal items. In the article six methods were applied to construct separate forecasting systems: Croston's, SBA (Syntetos–Boylan Approximation), TSB (Teunter, Syntetos, Babai), MA (Moving Average), SES (Simple Exponential Smoothing) and SESAP (Simple Exponential Smoothing for Analogous subPeriods). The latter method (SESAP) is an author's proposal dedicated for companies facing the problem of seasonal items. By analogous subperiods the same subperiods in each year are understood, for example, the same months in each year. A data set from the real company was used to apply all the above forecasting procedures. That data set contained monthly time series for about nine thousand products. The forecasts accuracy was tested by means of both parametric and non–parametric measures. The scaled mean and the scaled root mean squared error were used to check biasedness and efficiency. Also, the mean absolute scaled error and the shares of best forecasts were estimated. The general conclusion is that in the analyzed company a forecasting system should be based on two forecasting methods: TSB and SESAP, but the latter method should be applied only to seasonal items (products sold only in specific subperiods). It also turned out that Croston's and SBA methods work worse than much simpler methods, such as SES or MA. The presented analysis might be helpful for enterprises facing the problem of forecasting intermittent items (and seasonal intermittent items as well).
Resting state connectivity differences in eyes open versus eyes closed conditions
Authors: Agcaoglu Oktay , Wilson Tony W. , Wang Yu‐Ping , Stephen Julia , Calhoun Vince D.
Published: February 2019

Functional magnetic resonance imaging data are commonly collected during the resting state. Resting state functional magnetic resonance imaging (rs‐fMRI) is very practical and applicable for a wide range of study populations. Rs‐fMRI is usually collected in at least one of three different conditions/tasks, eyes closed (EC), eyes open (EO), or eyes fixated on an object (EO‐F). Several studies have shown that there are significant condition‐related differences in the acquired data. In this study, we compared the functional network connectivity (FNC) differences assessed via group independent component analysis on a large rs‐fMRI dataset collected in both EC and EO‐F conditions, and also investigated the effect of covariates (e.g., age, gender, and social status score). Our results indicated that task condition significantly affected a wide range of networks; connectivity of visual networks to themselves and other networks was increased during EO‐F, while EC was associated with increased connectivity of auditory and sensorimotor networks to other networks. In addition, the association of FNC with age, gender, and social status was observed to be significant only in the EO‐F condition (though limited as well). However, statistical analysis did not reveal any significant effect of interaction between eyes status and covariates. These results indicate that resting‐state condition is an important variable that may limit the generalizability of clinical findings using rs‐fMRI.
Glial Cell Line–Derived Neurotrophic Factor Enhances Autophagic Flux in Mouse and Rat Hepatocytes and Protects Against Palmitate Lipotoxicity
Authors: Mwangi Simon Musyoka , Li Ge , Ye Lan , Liu Yunshan , Reichardt Francois , Yeligar Samantha M. , Hart C. Michael , Czaja Mark J. , Srinivasan Shanthi
Published: February 2019

Glial cell line–derived neurotrophic factor (GDNF) is a protein that is required for the development and survival of enteric, sympathetic, and catecholaminergic neurons. We previously reported that GDNF is protective against high fat diet (HFD)‐induced hepatic steatosis in mice through suppression of hepatic expression of peroxisome proliferator activated receptor‐γ and genes encoding enzymes involved in de novo lipogenesis. We also reported that transgenic overexpression of GDNF in mice prevented the HFD‐induced liver accumulation of the autophagy cargo‐associated protein p62/sequestosome 1 characteristic of impaired autophagy. Here we investigated the effects of GDNF on hepatic autophagy in response to increased fat load, and on hepatocyte mitochondrial fatty acid β‐oxidation and cell survival. GDNF not only prevented the reductions in the liver levels of some key autophagy‐related proteins, including Atg5, Atg7, Beclin‐1 and LC3A/B‐II, seen in HFD‐fed control mice, but enhanced their levels after 12 weeks of HFD feeding. In vitro, GDNF accelerated autophagic cargo clearance in primary mouse hepatocytes and a rat hepatocyte cell line, and reduced the phosphorylation of the mechanistic target of rapamycin complex downstream‐target p70S6 kinase similar to the autophagy activator rapamycin. GDNF also enhanced mitochondrial fatty acid β‐oxidation in primary mouse and rat hepatocytes, and protected against palmitate‐induced lipotoxicity. Conclusion: We demonstrate a role for GDNF in enhancing hepatic autophagy and in potentiating mitochondrial function and fatty acid oxidation. Our studies show that GDNF and its receptor agonists could be useful for enhancing hepatocyte survival and protecting against fatty acid–induced hepatic lipotoxicity.
GITR ligation enhances functionality of tumor‐infiltrating T cells in hepatocellular carcinoma
Authors: van Beek Adriaan A. , Zhou Guoying , Doukas Michail , Boor Patrick P.C. , Noordam Lisanne , Mancham Shanta , Campos Carrascosa Lucia , van der Heide‐Mulder Marieke , Polak Wojciech G. , Ijzermans Jan N.M. , Pan Qiuwei , Heirman Carlo , Mahne Ashley , Bucktrout Samantha L. , Bruno Marco J. , Sprengers Dave , Kwekkeboom Jaap
Published: February 2019

No curative treatment options are available for advanced hepatocellular carcinoma (HCC). Anti‐PD1 antibody therapy can induce tumor regression in 20% of advanced HCC patients, demonstrating that co‐inhibitory immune checkpoint blockade has therapeutic potential for this type of cancer. However, whether agonistic targeting of co‐stimulatory receptors might be able to stimulate anti‐tumor immunity in HCC is as yet unknown. We investigated whether agonistic targeting of the co‐stimulatory receptor GITR could reinvigorate ex vivo functional responses of tumor‐infiltrating lymphocytes (TIL) freshly isolated from resected tumors of HCC patients. In addition, we compared GITR expression between TIL and paired samples of leukocytes isolated from blood and tumor‐free liver tissues, and studied the effects of combined GITR and PD1 targeting on ex vivo TIL responses. In all three tissue compartments, CD4+FoxP3+ regulatory T cells (Treg) showed higher GITR−expression than effector T‐cell subsets. The highest expression of GITR was found on CD4+FoxP3hiCD45RA− activated Treg in tumors. Recombinant GITR‐ligand as well as a humanized agonistic anti‐GITR antibody enhanced ex vivo proliferative responses of CD4+ and CD8+ TIL to tumor antigens presented by mRNA‐transfected autologous B‐cell blasts, and also reinforced proliferation, IFN‐γ secretion and granzyme B production in stimulations of TIL with CD3/CD28 antibodies. Combining GITR ligation with anti‐PD1 antibody nivolumab further enhanced tumor antigen‐specific responses of TIL in some, but not all, HCC patients, compared to either single treatment. In conclusion, agonistic targeting of GITR can enhance functionality of HCC TIL, and may therefore be a promising strategy for single or combinatorial immunotherapy in HCC.
Multi‐ATOM: Ultrahigh‐throughput single‐cell quantitative phase imaging with subcellular resolution
Authors: Lee Kelvin C. M. , Lau Andy K. S. , Tang Anson H. L. , Wang Maolin , Mok Aaron T. Y. , Chung Bob M. F. , Yan Wenwei , Shum Ho C. , Cheah Kathryn S. E. , Chan Godfrey C. F. , So Hayden K. H. , Wong Kenneth K. Y. , Tsia Kevin K.
Published: February 2019

A growing body of evidence has substantiated the significance of quantitative phase imaging (QPI) in enabling cost‐effective and label‐free cellular assays, which provides useful insights into understanding the biophysical properties of cells and their roles in cellular functions. However, available QPI modalities are limited by the loss of imaging resolution at high throughput and thus run short of sufficient statistical power at the single‐cell precision to define cell identities in a large and heterogeneous population of cells—hindering their utility in mainstream biomedicine and biology. Here we present a new QPI modality, coined multiplexed asymmetric‐detection time‐stretch optical microscopy (multi‐ATOM) that captures and processes quantitative label‐free single‐cell images at ultrahigh throughput without compromising subcellular resolution. We show that multi‐ATOM, based upon ultrafast phase‐gradient encoding, outperforms state‐of‐the‐art QPI in permitting robust phase retrieval at a QPI throughput of >10 000 cell/sec, bypassing the need for interferometry which inevitably compromises QPI quality under ultrafast operation. We employ multi‐ATOM for large‐scale, label‐free, multivariate, cell‐type classification (e.g. breast cancer subtypes, and leukemic cells vs peripheral blood mononuclear cells) at high accuracy (>94%). Our results suggest that multi‐ATOM could empower new strategies in large‐scale biophysical single‐cell analysis with applications in biology and enriching disease diagnostics.
Influence of poly‐l‐lysine molecular weight on antibacterial efficacy in polymer multilayer films
Authors: Alkekhia Dahlia , Shukla Anita
Published: February 2019

Antibacterial coatings can prevent and treat medical device‐associated infections. We examined the antibacterial properties of coatings assembled from poly‐l‐lysine (PLL) and hyaluronic acid (HA). PLL/HA films were fabricated using layer‐by‐layer assembly with three different PLL MWs, differentiated by number of repeat units, that is, 33, 91, and 407 (denoted by PLL30, PLL90, and PLL400). Films assembled with all three PLL MWs completely inhibited the growth of planktonic, gram‐positive Staphylococcus aureus and methicillin‐resistant S. aureus and gram‐negative Pseudomonas aeruginosa and Escherichia coli over a 24‐h exposure. All three film architectures also inhibited S. aureus attachment by ~60–70% compared to non‐film‐coated surfaces, likely attributed to significant film hydration and electrostatic repulsion due to HA. The true differences in antibacterial efficacy between different PLL MWs were observed upon repeated exposure of PLL/HA to S. aureus every 24 h. We found that PLL400 films lost the ability to inhibit planktonic S. aureus growth after one use while PLL30 and PLL90 films were effective over 4–5 and 9–13 repeated exposures, respectively. Our experiments indicated that differences in efficacy were related to low in‐film mobility of PLL400 and also agreed with dissolution timescales for PLL30 and PLL90 films. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1324–1339, 2019.
Discogenic Back Pain: Literature Review of Definition, Diagnosis, and Treatment
Authors: Fujii Kengo , Yamazaki Masashi , Kang James D , Risbud Makarand V , Cho Samuel K , Qureshi Sheeraz A , Hecht Andrew C , Iatridis James C
Published: February 2019

Discogenic back pain is multifactorial; hence, physicians often struggle to identify the underlying source of the pain. As a result, discogenic back pain is often hard to treat—even more so when clinical treatment strategies are of questionable efficacy. Based on a broad literature review, our aim was to define discogenic back pain into a series of more specific and interacting pathologies, and to highlight the need to develop novel approaches and treatment strategies for this challenging and unmet clinical need. Discogenic pain involves degenerative changes of the intervertebral disc, including structural defects that result in biomechanical instability and inflammation. These degenerative changes in intervertebral discs closely intersect with the peripheral and central nervous systems to cause nerve sensitization and ingrowth; eventually central sensitization results in a chronic pain condition. Existing imaging modalities are nonspecific to pain symptoms, whereas discography methods that are more specific have known comorbidities based on intervertebral disc puncture and injection. As a result, alternative noninvasive and specific diagnostic methods are needed to better diagnose and identify specific conditions and sources of pain that can be more directly treated. Currently, there are many treatments/interventions for discogenic back pain. Nevertheless, many surgical approaches for discogenic pain have limited efficacy, thus accentuating the need for the development of novel treatments. Regenerative therapies, such as biologics, cell‐based therapy, intervertebral disc repair, and gene‐based therapy, offer the most promise and have many advantages over current therapies. © 2019 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research
SiMPLOD, a Structure-Integrated Database of Collagen Lysyl Hydroxylase (LH/PLOD) Enzyme Variants
Authors: Scietti Luigi , Campioni Matteo , Forneris Federico
Published: February 2019

PLOD genes encode for procollagen lysyl hydroxylase enzymes (LH/PLOD), a family of proteins essential for collagen biosynthesis. Several mutations affect these genes, causing severe disorders, such as Ehlers-Danlos and Bruck syndrome, as well a connective tissue disease with phenotype resembling osteogenesis imperfecta caused by lack of LH3 functions. The recently determined three-dimensional (3D) structures of the full-length human LH3/PLOD3 isoform, together with the structure of a fragment of a viral LH/PLOD homolog, are now allowing molecular mapping of the numerous disease-causing mutations, providing insights often suitable for the interpretation of the resulting disease phenotypes. However, the added value of molecular structure interpretation is affected by the limited accessibility of complex molecular data to scientific communities lacking direct expertise in structural biology. In this work, we present a Structurally-integrated database for Mutations of PLOD genes (SiMPLOD), a publicly-available manually-curated online database with an embedded molecular viewer interface for the visualization and interpretation of LH/PLOD mutations on available molecular models. Each SiMPLOD entry is accompanied by manual annotations extrapolated from literature references and comments about the localization of the amino acid variants on the molecular structure. Additional links to the appropriate online resources for clinically-relevant as well as biochemical data are also provided in a standardized format. The web application is available at http://fornerislab.unipv.it/SiMPLOD. © 2019 American Society for Bone and Mineral Research.
The IMPACT study: early loss of skeletal muscle mass in advanced pancreatic cancer patients
Authors: Basile Debora , Parnofiello Annamaria , Vitale Maria Grazia , Cortiula Francesco , Gerratana Lorenzo , Fanotto Valentina , Lisanti Camilla , Pelizzari Giacomo , Ongaro Elena , Bartoletti Michele , Garattini Silvio Ken , Andreotti Victoria Josephine , Bacco Anna , Iacono Donatella , Bonotto Marta , Casagrande Mariaelena , Ermacora Paola , Puglisi Fabio , Pella Nicoletta , Fasola Gianpiero , Aprile Giuseppe , Cardellino Giovanni G.
Published: February 2019

Background

Pancreatic cancer (PC) patients have multiple risk factors for sarcopenia and loss of skeletal muscle mass (LSMM), which may cause greater treatment toxicities, reduced response to cancer therapy, prolonged hospitalization, impaired quality of life, and worse prognosis.

Methods

This is a retrospective study on advanced PC patients treated at the Department of Oncology of Udine, Italy, from January 2012 to November 2017. Among 162 patients who received chemotherapy, 94 consecutive patients with an available computed tomography (CT) scan were retrospectively analyzed. The primary objective of our study was to explore if an early LSMM ≥ 10% (measured at first radiological evaluation and compared with baseline) and/or baseline sarcopenia may impact prognosis. Baseline sarcopenia was defined according to Prado's criteria. Skeletal muscle area was measured as cross‐sectional areas (cm2) using CT scan data through the Picture archiving and communication system (PACS) image system.

Results

In the whole cohort, 48% of patients were ≤70 years old, and 50% had metastatic disease.

At baseline, 73% of patients had sarcopenia, and 16% presented a visceral fat area ≥ 44 cm2/m2. Overall, 21% experienced an early LSMM ≥ 10%. Approximately 33% of sarcopenic patients at baseline and ~35% of patients with early LSMM ≥ 10% had a body mass index > 25 kg/m2. Of note, 71% of patients were evaluated by a nutritionist, and 56% received a dietary supplementation (oral and/or parenteral). After a median follow‐up of 30.44 months, median overall survival (OS) was 11.28 months, whereas median progression‐free survival (PFS) was 5.72 months. By multivariate analysis, early LSMM ≥ 10% was significantly associated with worse OS [hazard ratio (HR): 2.16; 95% confidence interval (CI) 1.23–3.78; P = 0.007] and PFS (HR: 2.31; 95% CI 1.30–4.09; P = 0.004). Moreover, an exploratory analysis showed that inflammatory indexes, such as neutrophil–lymphocyte ratio variation, impact early LSMM ≥ 10% (odds ratio 1.31, 95% CI 1.06–1.61, P = 0.010).

Conclusions

Early LSMM ≥ 10% has a negative prognostic role in advanced PC patients. Further prospective investigations are needed to confirm these preliminary data.
Frontline Science: TNF-α and GM-CSF1 priming augments the role of SOS1/2 in driving activation of Ras, PI3K-γ, and neutrophil proinflammatory responses
Authors: Suire Sabine , Baltanas Fernando C , Segonds-Pichon Anne , Davidson Keith , Santos Eugenio , Hawkins Phillip T , Stephens Len R
Published: February 2019

Circulating neutrophils are, by necessity, quiescent and relatively unresponsive to acute stimuli. In regions of inflammation, mediators can prime neutrophils to react to acute stimuli with stronger proinflammatory, pathogen-killing responses. In neutrophils G protein-coupled receptor (GPCR)-driven proinflammatory responses, such as reactive oxygen species (ROS) formation and accumulation of the key intracellular messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3), are highly dependent on PI3K-γ, a Ras-GTP, and Gβγ coincidence detector. In unprimed cells, the major GPCR-triggered activator of Ras is the Ras guanine nucleotide exchange factor (GEF), Ras guanine nucleotide releasing protein 4 (RasGRP4). Although priming is known to increase GPCR–PIP3 signaling, the mechanisms underlying this augmentation remain unclear. We used genetically modified mice to address the role of the 2 RasGEFs, RasGRP4 and son of sevenless (SOS)1/2, in neutrophil priming. We found that following GM-CSF/TNFα priming, RasGRP4 had only a minor role in the enhanced responses. In contrast, SOS1/2 acquired a substantial role in ROS formation, PIP3 accumulation, and ERK activation in primed cells. These results suggest that SOS1/2 signaling plays a key role in determining the responsiveness of neutrophils in regions of inflammation.
The emerging roles of macrophages in cancer metastasis and response to chemotherapy
Authors: Sanchez Luis Rivera , Borriello Lucia , Entenberg David , Condeelis John S , Oktay Maja H , Karagiannis George S
Published: February 2019

Macrophages represent a heterogeneous group of cells, capable of carrying out distinct functions in a variety of organs and tissues. Even within individual tissues, their functions can vary with location. Tumor-associated macrophages (TAMs) specialize into three major subtypes that carry out multiple tasks simultaneously. This is especially true in the context of metastasis, where TAMs establish most of the cellular and molecular prerequisites for successful cancer cell dissemination and seeding to the secondary site. Perivascular TAMs operate in the perivascular niche, where they promote tumor angiogenesis and aid in the assembly of intravasation sites called tumor microenvironment of metastasis (TMEM). Streaming TAMs co-migrate with tumor cells (irrespective of the perivascular niche) and promote matrix remodeling, tumor cell invasiveness, and an immunosuppressive local microenvironment. Premetastatic TAMs are recruited to the premetastatic niche, where they can assist in tumor cell extravasation, seeding, and metastatic colonization. The dynamic interplay between TAMs and tumor cells can also modify the ability of the latter to resist cytotoxic chemotherapy (a phenotype known as environment-mediated drug resistance) and induce chemotherapy-mediated pro-metastatic microenvironmental changes. These observations suggest that future therapeutics should be designed to target TAMs with the aim of suppressing the metastatic potential of tumors and rendering chemotherapy more efficient.
The pre‐separation of oxygen containing compounds in oxidised heavy paraffinic fractions and their identification by GC‐MS with supersonic molecular beams.
Authors: Potgieter Hein , de Coning Piet , Bekker Riaan , Rohwer Egmont , Amirav Aviv
Published: February 2019

The heavy petroleum fractions produced during refining processes need to be upgraded to useable products to increase their value. Hydrogenated heavy paraffinic fractions can be oxidised to produce high value products that contain a variety of oxygenates. These heavy oxygenated paraffinic fractions need to be characterised to enable the control of oxidation processes and to understand product properties. The accurate identification of the oxygenates present in these fractions by electron ionisation (EI) mass spectrometry is challenging due to the complexity of these heavy fractions. Adding to this challenge is the limited applicability of EI mass spectral libraries due to the absence of molecular ions from the EI mass spectra of many oxygenates. The separation of oxygenates from the complex hydrocarbon matrix prior to high temperature GC‐MS (HT‐GC‐MS) analysis reduces the complexity of these fractions and assists in the accurate identification of these oxygenates. Solid phase extraction (SPE) and supercritical fluid chromatography (SFC) were employed as prefractionation techniques. GC‐MS with supersonic molecular beams (SMBs) (also named GC‐MS with cold‐EI) utilises a SMB interface with which EI is done with vibrationally cold sample compounds in a fly‐through ion source (cold‐EI) resulting in a substantial increase in the molecular ion signal intensity in the mass spectrum. This greatly enhances the accurate identification of the oxygenates in these fractions. This study investigated the ionisation behaviour of oxygenated compounds using cold‐EI. The prefractionation by SPE and SFC and the subsequent analysis with GC‐MS with cold‐EI were applied to an oxygenated heavy paraffinic fraction.
Effect of anatomical variability on stress‐shielding induced by short calcar‐guided stems: Automated finite element analysis of 90 femora
Authors: Sas Amelie , Pellikaan Pim , Kolk Sjoerd , Marty Pablo , Scheerlinck Thierry , van Lenthe G. Harry
Published: February 2019

Short stem hip implants are becoming increasingly popular since they preserve bone stock and presumably reduce stress‐shielding. However, concerns remain whether they are suitable for a wide range of patients with varying anatomy. The aim of this study was to investigate how femoral anatomy influences stress‐shielding induced by a short calcar‐guided stem across a set of 90 CT‐based femur models. A computational tool was developed that automatically selected the optimal size and position of the stem. Finite element models of the intact and implanted femurs were constructed and subjected to walking loads. Stress‐shielding was evaluated in relevant volumes of interest of the proximal femur. After a detailed anatomical analysis, linear regression was performed to find potential correlations between anatomy and stress‐shielding. Stress‐shielding was found to be highest in the proximal regions on the medial and posterior side. A highly significant negative relationship was observed between stress‐shielding and bone density; a strong positive relationship was observed with stem size and the valgus orientation of the stem with respect to the femur. The results reveal how anatomy influences stress‐shielding, and they highlight the importance of evaluating new implant designs across a large population taking into account the anatomical variability. The study demonstrates that such large population studies can be conducted in an efficient way using an automated workflow. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 9999:1–8, 2019.
Andosol clay re‐aggregation observed at the microscale during physical organic matter fractionation
Authors: Inagaki Thiago M. , Mueller Carsten W. , Lehmann Johannes , Kögel-Knabner Ingrid
Published: February 2019

The high aggregate stability of Andosols and the direct effects of sample drying led to several inconsistencies during physical soil organic matter fractionation. We have determined that NaCl addition displayed little influence on clay dispersion. At the microscale, we observed the re‐aggregation of the clay fraction caused by freeze‐drying. This issue was avoided by analyzing aliquots of soil suspension. Thus, we recommend reserving a small soil liquid aliquot to be subjected to microscopy analysis.
Elk forage and risk tradeoffs during the fall archery season
Authors: DeVoe Jesse D. , Proffitt Kelly M. , Mitchell Michael S. , Jourdonnais Craig S. , Barker Kristin J.
Published: February 2019

During late summer and fall, elk (Cervus canadensis) need access to adequate nutrition to support physiological requirements for reproduction and overwinter survival. The archery hunting season often occurs during this period and can affect distributions of elk as they seek areas that minimize perceived harvest risk. Areas that confer lower harvest risk may provide relatively low‐value nutrition, resulting in a potential tradeoff between minimizing risk and accessing adequate forage. We used radio‐collar data collected from female elk during late summer and fall (Aug–Oct) and estimated resource selection models to evaluate the extent of this potential risk‐nutrition tradeoff. To evaluate if elk exposed to a greater hunting risk altered selection for forage resources, we assessed the relationship between individuals’ selection coefficients for forage and the proportion of their late‐summer‐fall home range accessible to hunters (our metric of hunting risk). Our results indicate that during the archery season, elk with higher‐risk home ranges selected more strongly for areas farther from motorized routes than elk with lower‐risk home ranges. Regardless of the level of risk, however, elk maintained or increased selection for areas with higher forage quality, suggesting that elk did not compromise access to nutritional resources during the archery season. Elk with higher‐risk home ranges were also exposed to the poorest nutrition and increased their selection for areas with higher forage quality more strongly than elk with lower‐risk home ranges during the hunting season. Elk with lower‐risk home ranges had access to the highest nutrition, which may be due to the availability of concentrated sources of high‐quality forage from irrigated agricultural areas on private lands that restricted hunter access. Resource agencies interested in encouraging elk to remain on public lands during the hunting seasons might consider closing motorized travel during the archery season to increase security on public lands, limiting hunter pressure on public lands, improving forage quality on public lands, and working with private land owners to enhance hunter accessibility and restrict elk access to high‐quality forage resources. © 2019 The Wildlife Society.
Pelagic contribution to gross primary production dynamics in shallow areas of York River, VA, U.S.A.
Authors: Qin Qubin , Shen Jian
Published: February 2019

The pelagic contribution to total gross primary production (GPP) is often used to evaluate the assemblages of primary producers in shallow estuarine and coastal ecosystems that shift between benthic‐dominated and pelagic‐dominated status as a response to nutrient loading change. This study investigated the spatial and temporal variability of the pelagic contribution to ecosystem GPP for the years 2003–2015 in shallow areas of the York River. The monthly average values of ecosystem GPP and pelagic GPP were estimated by using 15‐min observational data of dissolved oxygen and chlorophyll a, respectively. A larger pelagic contribution, generally, corresponded to a higher pelagic GPP, while pelagic GPP showed significant positive correlations to riverine discharge and total nitrogen loading at mesohaline and polyhaline stations. The interannual variability in benthic GPP (ecosystem GPP – pelagic GPP), however, exhibited a non‐monotonic relationship to the increase in pelagic GPP. A conceptual model with four ecosystem stages in response to nutrient loading changes is proposed based on changes in the relationship between benthic GPP and pelagic GPP, and that between pelagic contribution and pelagic GPP. The model can explain the different responses of an ecosystem to nutrient loading observed in various estuaries and can be used to evaluate the status of an ecosystem undergoing the eutrophication/oligotrophication process. The stages of York River ecosystems during the study period were quantitatively examined. Results suggest that benthic GPP shows negative correlations to pelagic GPP in the downstream York River over most months of the year, indicating a gradual degradation of the benthic community.
Improved Cell Viability and Biocompatibility of Bacterial Cellulose through in Situ Carboxymethylation
Authors: Zhou Dongyan , Sun Yue , Bao Zixian , Liu Wenshuai , Xian Mo , Nian Rui , Xu Fei
Published: February 2019

Bacterial cellulose (BC) is a natural product with multiple properties, which has been utilized in tissue engineering. However, cell adhesion and proliferation are reported to be weaker on native BC, providing less support compared to other types of biomaterials, like collagen. To increase the biocompatibility and the medical performance of BC, in situ modification is used to add carboxymethyl group to BC. By partially changing the structure and physical properties of BC, carboxymethylation significantly increases cell affinity and viability, especially on the initial cell adhesion. Furthermore, in the in vivo implantation, the tissue reaction shows that carboxymethylation significantly increases the biocompatibility of BC, exhibiting better tissue condition and a lower inflammatory reaction which are proved through HE staining and immunohistochemistry. The data prove that in situ carboxymethylation is a simple and direct way of improving the performance of BC in medical applications.
Full asymptotics and Laurent series of layer potentials for Laplace's equation on the half‐space
Authors: Fritzsch Karsten
Published: February 2019

We combine the calculus of conormal distributions, in particular the Pull‐Back and Push‐Forward Theorems, with the method of layer potentials to solve the Dirichlet and Neumann problems on half‐spaces. We obtain full asymptotic expansions for the solutions, show that boundary layer potential operators are elements of the full b‐calculus and give a new proof of the classical jump relations. En route, we improve Siegel and Talvila's growth estimates for the modified layer potentials in the case of polyhomogeneous boundary data. The techniques we use here can be generalised to geometrically more complex settings, as for instance the exterior domain of touching domains or domains with fibred cusps. This work is intended to be a first step in a longer program aiming at understanding the method of layer potentials in the setting of certain non‐Lipschitz singularities that can be resolved in the sense of Melrose using manifolds with corners and at applying a matching asymptotics ansatz to singular perturbations of related problems.
Real hypersurfaces in the complex quadric whose structure Jacobi operator is of Codazzi type
Authors: Suh Young Jin
Published: February 2019

First we introduce the notion of structure Jacobi operator of Codazzi type for real hypersurfaces in the complex quadric . Next we give a complete classification of real hypersurfaces in with structure Jacobi operator of Codazzi type.
Identifying pathogenic variants in the Follistatin‐like 1 gene (FSTL1) in patients with skeletal and atrioventricular valve disorders
Authors: Prakash Stuti , Mattiotti Andrea , Sylva Marc , Mulder Barbara J. M. , Postma Alex V. , van den Hoff Maurice J. B.
Published: February 2019

Background

Follistatin‐like 1 (Fstl1) is a glycoprotein expressed throughout embryonic development. Homozygous loss of Fstl1 in mice results in skeletal and respiratory defects, leading to neonatal death due to a collapse of the trachea. Furthermore, Fstl1 conditional deletion from the endocardial/endothelial lineage results in postnatal death due to heart failure and profound atrioventricular valve defects. Here, we investigated patients with phenotypes similar to the phenotypes observed in the transgenic mice, for variants in FSTL1.

Methods

In total, 69 genetically unresolved patients were selected with the following phenotypes: campomelic dysplasia (12), small patella syndrome (2), BILU (1), and congenital heart disease patients (54), of which 16 also had kyphoscoliosis, and 38 had valve abnormalities as their main diagnosis. Using qPCR, none of 69 patients showed copy number variations in FSTL1. The entire gene body, including microRNA‐198 and three validated microRNA‐binding sites, were analyzed using Sanger sequencing.

Results

No variants were found in the coding region. However, 8 intronic variants were identified that differed significantly in their minor allele frequency compared to controls. Variant rs2272515 was found to significantly correlate (p < 0.05) with kyphoscoliosis.

Conclusion

We conclude that pathogenic variants in FSTL1 are unlikely to be responsible for skeletal or atrioventricular valve anomalies in humans.
Health center's process improvement dramatically boosts depression care
Authors: Enos Gary
Published: February 2019

A federally qualified health center (FQHC) in rural central Virginia has demonstrated that depression screening and follow‐up can be dramatically improved in a multicultural community where stigma remains a significant influence. The Harrisonburg Community Health Center achieved this through a rapid‐cycle improvement process that shattered a number of assumptions about its patient population.
Lack of housing for released inmates with SMI prompts lawsuit
Authors: Canady Valerie A.
Published: February 2019

Alleging practices of keeping New York offenders with mental illness incarcerated past their release date due to lack of community‐based housing and supportive services, New York advocates on Jan. 23 filed a federal class action lawsuit in U.S. District Court against Gov. Andrew Cuomo and state officials.
Research finds incarcerated youth more prone to suicide
Authors: Canady Valerie A.
Published: February 2019

Observing that more youth in confinement die by suicide than any other reported cause of death, new research into the high rates of suicide for incarcerated teens supports the need for improved suicide risk assessment and safety planning and interventions tailored to the specific incarceration setting, say researchers. The study was published Jan. 23 in the Journal of the American Academy of Child & Adolescent Psychiatry.
Field trial of IRNSS receiver
Authors: Rawat Abhishek , Savaliya Jatin , Chhabhaya Dwarkesh
Published: February 2019

IRNSS is an independent regional navigation system being developed by Indian Space Research Organization, India. Ionospheric scintillations are very important to satellite‐based radio communication and navigation. Ionospheric variations are responsible for most of the range error which yields in inaccurate position coordinates and degradation in signal power (carrier to noise power ratio).This article represents a comparative analysis of position error and Ionospheric delay among IRNSS (Indian Regional Navigation Satellite System) and GPS (Global Positioning System) considering the ionospheric correction algorithms being used in both satellite constellations. Grid based ionospheric correction, dual frequency delay correction, and coefficient based have been considered for comparison of both IRNSS and GPS navigation system.
Reducing false positive rate of fetal monosomy X in non‐invasive prenatal testing using a combined algorithm to detect maternal mosaic monosomy X
Authors: Phan Minh‐Duy , Vo Binh T. , Nguyen Thong V. , Tran Nhat‐Thang , Trinh Huong N.T. , Nguyen Tho T.Q. , Nguyen Nguyen H. , Tran Truong T. , Tran Uyen V. , Dao Thuy T.H. , Pham Anh H. , Tran Tam H. , Truong Kiet D. , Hoang Tuyet T.D. , Do Thanh‐Thuy T. , Nguyen Hoai‐Nghia , Giang Hoa
Published: February 2019

What's already known about this topic?

The false positive rate of detecting monosomy X by NIPT is higher than that of other autosomal aneuploidies, due in part to maternal mosaic monosomy X.

What does this study add?

Our triSure method is less sensitive to the confounding effect of maternal DNA than NIPTeR method.

By combining z‐scores of chrX from triSure and NIPTeR, we can detect cases of fetal XX (−2.5 < zX by triSure < 2.5) with maternal mosaicism monosomy X (zX by NIPTeR < −2.5), potentially reducing false positive rate of fetal monosomy X.
Variants in the 5'‐UTR of APELA gene in women with preeclampsia
Authors: Yang Xin , Bian Yuehong , Wan Jipeng , Li Lei , Yang Ping , Zhao Shigang , Zhao Han
Published: February 2019

Objective

To detect APELA gene variants in clinical cases with preeclampsia (PE) and evaluate the influence of the APELA variants in gene expression.

Method

A total of 288 individuals suffering from PE and 384 unaffected individuals were chosen for case‐control studies. Genomic DNA was extracted from peripheral blood. Variants screening of APELA gene was conducted, and potential influence of variants in APELA expression was evaluated with a luciferase assay.

Results

Two rare variants (c.‐306A > G and c.‐145A > G) in the 5'‐UTR of APELA gene were identified exclusively in PE affected individuals. Luciferase assays in HEK293 cells and HTR‐8/SVneo cells revealed that both variants impaired transcriptional activity of APELA by altering the function of promoter region. Also, a single‐nucleotide polymorphism (SNP) (c.159 T > C) in exon 2 of APELA was found in both cases and controls, and there was no statistically significant difference in genotype and allele frequency between cases and controls.

Conclusion

Variants in the 5'‐UTR of APELA gene may account for variability of APELA expression among individuals with PE and may play a negative regulatory role in the pathogenesis of PE.
Validating an algorithm for multiple myeloma based on administrative data using a SEER tumor registry and medical record review
Authors: Brandenburg Nancy A. , Phillips Syd , Wells Karen E. , Woodcroft Kimberley J. , Amend Kandace L. , Enger Cheryl , Oliveria Susan A.
Published: February 2019

Purpose

Large numbers of multiple myeloma patients can be studied in real‐world clinical settings using administrative databases. The validity of these studies is contingent upon accurate case identification. Our objective was to develop and evaluate algorithms to use with administrative data to identify multiple myeloma cases.

Methods

Patients aged ≥18 years with ≥1 International Classification of Diseases, 9th Revision, Clinical Modification (ICD‐9‐CM) code for multiple myeloma (203.0x) were identified at two study sites. At site 1, several algorithms were developed and validated by comparing results to tumor registry cases.

An algorithm with a reasonable positive predictive value (PPV) (0.81) and sensitivity (0.73) was selected and then validated at site 2 where results were compared with medical chart data. The algorithm required that ICD‐9‐CM codes 203.0x occur before and after the diagnostic procedure codes for multiple myeloma.

Results

At site 1, we identified 1432 patients. The PPVs of algorithms tested ranged from 0.54 to 0.88. Sensitivities ranged from 0.30 to 0.88. At site 2, a random sample (n = 400) was selected from 3866 patients, and medical charts were reviewed by a clinician for 105 patients. Algorithm PPV was 0.86 (95% CI, 0.79‐0.92).

Conclusions

We identified cases of multiple myeloma with adequate validity for claims database analyses. At least two ICD‐9‐CM diagnosis codes 203.0x preceding diagnostic procedure codes for multiple myeloma followed by ICD‐9‐CM codes within a specific time window after diagnostic procedure codes were required to achieve reasonable algorithm performance.
Circumventing the pole problem of reduced lat‐lon grids with local schemes. Part II: Validation experiments
Authors: Glinton Michael R. , Bénard Pierre
Published: February 2019

Conditions for a horizontal discretization scheme to circumvent the pole problem of reduced latitude–longitude grids in spherical coordinates have been determined in Part I, and a forecast model built on these principles (GRASS) has been developed to solve the shallow‐water equations on the sphere with various accuracy orders in space. Validation experiments are presented here with the main goal to assess the capacity of the model to perform stable, smooth and accurate forecasts with weak filter strengths, even at very high resolution. The selection of test‐cases presented here includes a stationary solid‐body rotation flow over the poles, and a stationary parallel flow with a curved profile of the velocity at poles. A demanding recently proposed test‐case is finally examined in detail, for non‐rotated and rotated coordinates. All test results indicate that the model is able to reach the initial objectives.
A numerical simulation of a strong wind event in January 2013 at King Sejong station, Antarctica
Authors: Kwon Hataek , Park Sang‐Jong , Lee Solji , Kim Baek‐Min , Choi Taejin , Kim Seong‐Joong
Published: February 2019

A strong wind event (SWE), so‐called “severe gale”, with a 10 min average wind speed of above 22 m/s occurred on 7 January 2013 at the King Sejong station (KSJ) on the tip of the Antarctic Peninsula (AP). We examine the cause of the SWE and assess the short‐term predictability of such an event, using the state‐of‐the‐art Polar Weather Research and Forecasting (Polar WRF) model. The simulation results, initialized at 0000 UTC 6 January 2013, the day prior to the occurrence of the SWE, produce the most accurate representation of the SWE in terms of strength (∼94% of the peak wind speed). Both model results and observational records reveal that the SWE is mainly caused by the approach of a deep depression with the central pressure of 950 hPa. On top of this synoptic configuration, a particular shape of topography of the AP plays a non‐negligible role for further intensification of the wind at KSJ. As the cyclone approaches the AP, the sea‐level pressure becomes lower and is deformed around the AP due to the topography, driving southeasterly winds traversing the AP. The continuous flow overriding the AP generates a downslope windstorm at the lee side of the AP. The windstorm effect driven by the deformation of sea‐level pressure by the topography of the AP is not properly represented in the coarser‐resolution (27 km) model domain compared with higher (3 and 9 km) resolutions. We conclude that the SWE at KSJ on 7 January 2013 is caused by the combined effect of a synoptic‐scale low‐pressure system with local topography of the AP.
Chemical machine learning with kernels: The impact of loss functions
Authors: Nguyen Quang Van , De Sandip , Lin Junhong , Cevher Volkan
Published: February 2019

Machine learning promises to accelerate materials discovery by allowing computational efficient property predictions from a small number of reference calculations. As a result, the literature has spent a considerable effort in designing representations that capture basic physical properties. Our work focuses on the less‐studied learning formulations in this context in order to exploit inner structures in the prediction errors. In particular, we propose to directly optimize basic loss functions of the prediction error metrics typically used in the literature, such as the mean absolute error or the worst case error. In some instances, a proper choice of the loss function can directly reduce reasonably the prediction performance in the desired metric, albeit at the cost of additional computations during training. To support this claim, we describe the statistical learning theoretic foundations, and provide supporting numerical evidence with the prediction of atomization energies for a database of small organic molecules.