bluuebunny/crossref_metadata_2025_split huggingface dataset:
The central role of peripheral nodes in directed network dynamics
Authors: Wright Edgar A. P. , Yoon Sooyeon , Ferreira António L. , Mendes José F. F. , Goltsev Alexander V. 
Published: September 2019

AbstractMany social, technological, and biological systems with asymmetric interactions display a variety of collective phenomena, such as opinion formation and synchronization. This has motivated much research on the dynamical impact of local and mesoscopic structure in directed networks. However, the unique constraints imposed by the global organization of directed networks remain largely undiscussed. Here, we control the global organization of directed Erdős–Rényi networks, and study its impact on the emergence of synchronization and ferromagnetic ordering, using Kuramoto and Ising dynamics. In doing so, we demonstrate that source nodes – peripheral nodes without incoming links – can disrupt or entirely suppress the emergence of collective states in directed networks. This effect is imposed by the bow-tie organization of directed networks, where a large connected core does not uniquely ensure the emergence of collective states, as it does for undirected networks.
Prevalence and Risk Factors of Thyroid Dysfunction in Older Adults in the Community
Authors: Diab Nermin , Daya Natalie R. , Juraschek Stephen P. , Martin Seth S. , McEvoy John W. , Schultheiß Ulla T. , Köttgen Anna , Selvin Elizabeth 
Published: September 2019

AbstractPrevalence estimates and evidence informing treatment targets for thyroid dysfunction largely come from studies of middle-aged adults. We conducted a cross-sectional analysis to determine the prevalence of thyroid dysfunction and risk factors for abnormal thyroid tests in participants aged ≥65 in the Atherosclerosis Risk in Communities (ARIC) study (N = 5,392). We measured serum concentrations of triiodothyronine (T3), free thyroxine (FT4), thyroid peroxidase antibody (Anti-TPO), and thyroid stimulating hormone (TSH). In this population (58% women, 22% black), 17% reported medication use for thyroid dysfunction. Among those not on treatment, the prevalence of overt and subclinical hypothyroidism was 0.82% and 6.06%, respectively. Overt and subclinical hyperthyroidism affected 0.26% and 0.78%, respectively. Multivariable adjusted TSH, FT4 and T3 levels were 25%, 1.3% and 3.9% lower in blacks compared to whites, respectively. Men were less likely to be anti-TPO positive compared to women (p < 0.001). Former and never smoking were associated with lower T3 and FT4 levels compared to current smoking. The prevalence of thyroid dysfunction in older adults is nearly 25%. Multiple illnesses can interact to contribute to declines in health. Additional attention to thyroid dysfunction and screening in this age group is recommended.
A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes
Authors: Félix Carina , Meneses Rodrigo , Gonçalves Micael F. M. , Tilleman Laurentijn , Duarte Ana S. , Jorrín-Novo Jesus V. , Van de Peer Yves , Deforce Dieter , Van Nieuwerburgh Filip , Esteves Ana C. , Alves Artur 
Published: September 2019

AbstractLasiodiplodia theobromae (Botryosphaeriaceae, Ascomycota) is a plant pathogen and human opportunist whose pathogenicity is modulated by temperature. The molecular effects of temperature on L. theobromae are mostly unknown, so we used a multi-omics approach to understand how temperature affects the molecular mechanisms of pathogenicity. The genome of L. theobromae LA-SOL3 was sequenced (Illumina MiSeq) and annotated. Furthermore, the transcriptome (Illumina TruSeq) and proteome (Orbitrap LC-MS/MS) of LA-SOL3 grown at 25 °C and 37 °C were analysed. Proteins related to pathogenicity (plant cell wall degradation, toxin synthesis, mitogen-activated kinases pathway and proteins involved in the velvet complex) were more abundant when the fungus grew at 25 °C. At 37 °C, proteins related to pathogenicity were less abundant than at 25 °C, while proteins related to cell wall organisation were more abundant. On the other hand, virulence factors involved in human pathogenesis, such as the SSD1 virulence protein, were expressed only at 37 °C. Taken together, our results showed that this species presents a typical phytopathogenic molecular profile that is compatible with a hemibiotrophic lifestyle. We showed that L. theobromae is equipped with the pathogenesis toolbox that enables it to infect not only plants but also animals.
Enamel peptides reveal the sex of the Late Antique ‘Lovers of Modena’
Authors: Lugli Federico , Di Rocco Giulia , Vazzana Antonino , Genovese Filippo , Pinetti Diego , Cilli Elisabetta , Carile Maria Cristina , Silvestrini Sara , Gabanini Gaia , Arrighi Simona , Buti Laura , Bortolini Eugenio , Cipriani Anna , Figus Carla , Marciani Giulia , Oxilia Gregorio , Romandini Matteo , Sorrentino Rita , Sola Marco , Benazzi Stefano 
Published: September 2019

AbstractRecent work has disclosed the critical role played by enamel peptides in sex classification of old skeletal remains. In particular, protein AMELY (amelogenin isoform Y) is present in the enamel dental tissue of male individuals only, while AMELX (isoform X) can be found in both sexes. AMELY can be easily detected by LC-MS/MS in the ion extracted chromatograms of the SM(ox)IRPPY peptide (monoisotopic [M + 2 H]+2 mass = 440.2233 m/z). In this paper, we exploited the dimorphic features of the amelogenin protein to determine the sex of the so-called ‘Lovers of Modena’, two Late Antique individuals whose skeletons were intentionally buried hand-in-hand. Upon discovery, mass media had immediately assumed they were a male-female couple, even if bad preservation of the bones did not allow an effective sex classification. We were able to extract proteins from the dental enamel of both individuals (~1600 years old) and to confidently classify them as males. Results were compared to 14 modern and archaeological control samples, confirming the reliability of the ion chromatogram method for sex determination. Although we currently have no information on the actual relationship between the ‘Lovers of Modena’ (affective? Kin-based?), the discovery of two adult males intentionally buried hand-in-hand may have profound implications for our understanding of funerary practices in Late Antique Italy.
Minimal intervening control of biomolecular networks leading to a desired cellular state
Authors: Choo Sang-Mok , Park Sang-Min , Cho Kwang-Hyun 
Published: September 2019

AbstractA cell phenotype can be represented by an attractor state of the underlying molecular regulatory network, to which other network states eventually converge. Here, the set of states converging to each attractor is called its basin of attraction. A central question is how to drive a particular cell state toward a desired attractor with minimal interventions on the network system. We develop a general control framework of complex Boolean networks to provide an answer to this question by identifying control targets on which one-time temporary perturbation can induce a state transition to the boundary of a desired attractor basin. Examples are shown to illustrate the proposed control framework which is also applicable to other types of complex Boolean networks.
Aflatoxin levels in maize and peanut and blood in women and children: The case of Timor-Leste
Authors: de Almeida Luis , Williams Robert , Soares Dirce M. , Nesbitt Harry , Wright Graeme , Erskine William 
Published: September 2019

AbstractAflatoxins are toxic fungal metabolites produced byAspergillussp. with carcinogenic properties that are a common food contaminant of many crops including maize and peanuts. In Timor-Leste malnutrition and children’s stunting are frequent and maize and peanuts are staple foods. This study aimed to provide information on aflatoxin exposure nationally. The study measured levels of aflatoxin in locally-produced maize and peanuts (296 samples) and of aflatoxin-albumin conjugate in blood samples of women and young children (514 and 620 respectively) across all municipalities. The average concentration of aflatoxin in the grain samples was low with most maize (88%) and peanut (92%) samples - lower than European Commission tolerated aflatoxin level. Although aflatoxin–albumin conjugate was detected in more than 80% of blood samples, the average concentration in children and adults of 0.64 and 0.98 pg mg−1alb, respectively, is much lower than in other similar rural-based countries. Although low in concentration, blood aflatoxin levels and aflatoxin contamination levels in maize across municipalities were correlated significantly for mothers (R2 = 37%, n = 495) but not for children (R2 = 10%). It is unlikely that the consumption of aflatoxin contaminated grain is a causative factor in the current level of malnutrition and stunting affecting Timor-Leste children.
The Concavity of the Maximal Expiratory Flow–Volume Curve Reflects the Extent of Emphysema in Obstructive Lung Diseases
Authors: Mochizuki Fumi , Iijima Hiroaki , Watanabe Azusa , Tanabe Naoya , Sato Susumu , Shiigai Masanari , Fujiwara Keiji , Shimada Takafumi , Ishikawa Hiroichi , Kanazawa Jun , Yatagai Yohei , Masuko Hironori , Sakamoto Tohru , Muro Shigeo , Hizawa Nobuyuki 
Published: September 2019

AbstractA concave-shaped maximal expiratory flow-volume (MEFV) curve is a spirometric feature in chronic obstructive pulmonary disease (COPD). The MEFV curve is characterized by an increase in the Obstructive Index, which is defined as a ratio of forced vital capacity to the volume-difference between two points of half of the peak expiratory flow on the MEFV curve. We hypothesized that the Obstructive Index would reflect the severity of emphysema in patients with COPD and asthma-COPD overlap (ACO). Thus, the aim of this retrospective study was to evaluate whether the Obstructive Index on spirometry is associated with the extent of emphysema on computed tomography (CT) in patients with COPD, ACO, and asthma (N = 65, 15, and 53, respectively). The percentage of low-attenuation volume (LAV%) and wall area (WA%) were measured on CT. The Obstructive Index was higher in patients with COPD and ACO than in those with asthma. Spearman correlation showed that a greater Obstructive Index was associated with a higher LAV%, but not WA%. Multivariate analysis showed that Obstructive Index was associated with LAV% (standardized β = 0.43, P < 0.0001) independent of other spirometric indices. The Obstructive Index is a useful spirometric index that reflects the extent of emphysema.
Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules
Authors: Yanagi Itaru , Akahori Rena , Takeda Ken-ichi 
Published: September 2019

AbstractFor nanopore sensing of various-sized molecules with high sensitivity, the size of the nanopore should be adjusted according to the size of each target molecule. For solid-state nanopores, a simple and inexpensive nanopore fabrication method utilizing dielectric breakdown of a membrane is widely used. This method is suitable for fabricating a small nanopore. However, it suffers two serious problems when attempting to fabricate a large nanopore: the generation of multiple nanopores and the non-opening failure of a nanopore. In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. Moreover, the ionic-current blockades derived from streptavidin-labelled and non-labelled DNA passing through the fabricated nanopore were clearly distinguished. The current blockades caused by streptavidin-labelled DNA could be identified even when its concentration is 1% of the total DNA.
21-Gene Recurrence Score and Adjuvant Chemotherapy Decision for Breast Cancer Patients with Positive Lymph Nodes
Authors: Tong Yiwei , Wu Jiayi , Huang Ou , He Jianrong , Zhu Li , Chen Weiguo , Li Yafen , Chen Xiaosong , Shen Kunwei 
Published: September 2019

AbstractThe 21-gene recurrence score (RS) assay is prognostic and predictive for hormone receptor (HR)+/HER2-/node- breast cancer (BC) patients. However, its clinical value in node + patients hasn’t been elucidated. HR+/HER2-/pN1 patients operated in Comprehensive Breast Health Center, Shanghai Ruijin Hospital from January 2014 to December 2018, with available RS results were retrospectively included. Clinico-pathological characteristics were compared. Adjuvant chemotherapy recommendations pre-/post- RS assay and actual usage were analyzed. A total of 303 patients were included, with 59, 178, 66 RS < 18, 18–30 and ≥ 31. Age (P < 0.001), comorbidity (P = 0.013), and RS category (P < 0.001) were independently associated with chemotherapy recommendation. Compared with low RS patients, those with intermediate (OR 6.58, 95% CI 2.37–18.31, P < 0.001) or high (OR 54.14, 95% CI 3.77–776.54, P = 0.003) RS were more likely to be recommended with chemotherapy. RS independently influence chemotherapy decision in postmenopausal population as well. Chemotherapy recommendation changed for 9.57% patients after RS assay. Patient adherence rate to chemotherapy recommendation was 94.72% (287/303). The 21-gene RS independently influenced chemotherapy recommendation in pN1 BC patients, which could provide additional information to guide chemotherapy decision with relatively good treatment adherence rate.
Marginal diversity analysis of conservation of Chinese domestic duck breeds
Authors: Zhang Yang , Wang Laidi , Bian Youqing , Wang Zhaoshan , Xu Qi , Chang Guobin , Chen Guohong 
Published: September 2019

AbstractThe present study aimed to systematically evaluate the genetic diversity of Chinese domestic duck breeds and ensure the most effective allocation and usage of conservation funds. We first performed an analysis of DNA genetic distance in 21 duck breeds by measuring short tandem repeats. Then, we calculated the extinction probability, contribution rate, and marginal diversity for each breed. The results showed that the extinction rate of the Zhongshan duck, Guangxi duck, and Ji’an duck were the highest at 0.67, 0.59, and 0.59, respectively, and that of the Linwu duck, Jinding duck, and Gaoyou duck were the lowest at 0.15, 0.18, and 0.19, respectively. The current diversity of populations was 7.72 and the expected diversity in five hundred years is 5.14 ± 1.15. The marginal diversity of the Chinese Muscovy duck was the largest (−2.20), accounting for 42.61% of the expected diversity, followed by the Guangxi duck (−0.49, 9.44%), whereas the Jinding duck was the smallest (−0.12; 2.32%). The protection potency of the Chinese Muscovy duck was the largest (0.61), followed by Guangxi duck (0.29), whereas the Jinding duck was the smallest (0.02). This study provides a reference for determining the conservation priority of Chinese domestic duck breeds or genetic resources.
Chronic Pressure Overload Results in Deficiency of Mitochondrial Membrane Transporter ABCB7 Which Contributes to Iron Overload, Mitochondrial Dysfunction, Metabolic Shift and Worsens Cardiac Function
Authors: Kumar Vikas , A. Aneesh Kumar , Sanawar Rahul , Jaleel Abdul , Santhosh Kumar T. R. , Kartha C. C. 
Published: September 2019

AbstractWe examined the hitherto unexplored role of mitochondrial transporters and iron metabolism in advancing metabolic and mitochondrial dysfunction in the heart during long term pressure overload. We also investigated the link between mitochondrial dysfunction and fluctuation in mitochondrial transporters associated with pressure overload cardiac hypertrophy. Left ventricular hypertrophy (LVH) was induced in 3-month-old male Wistar rats by constriction of the aorta using titanium clips. After sacrifice at the end of 6 and 15 months after constriction, tissues from the left ventricle (LV) from all animals were collected for histology, biochemical studies, proteomic and metabolic profiling, and gene and protein expression studies. LV tissues from rats with LVH had a significant decrease in the expression of ABCB7 and mitochondrial oxidative phosphorylation (mt-OXPHOS) enzymes, an increased level of lipid metabolites, decrease in the level of intermediate metabolites of pentose phosphate pathway and elevated levels of cytoplasmic and mitochondrial iron, reactive oxygen species (ROS) and autophagy-related proteins. Knockdown of ABCB7 in H9C2 cells and stimulation with angiotensin II resulted in increased ROS levels, ferritin, and transferrin receptor expression and iron overload in both mitochondria and cytoplasm. A decrease in mRNA and protein levels of mt-OXPHOS specific enzymes, mt-dynamics and autophagy clearance and activation of IGF-1 signaling were also seen in these cells. ABCB7 overexpression rescued all these changes. ABCB7 was found to interact with mitochondrial complexes IV and V. We conclude that in chronic pressure overload, ABCB7 deficiency results in iron overload and mitochondrial dysfunction, contributing to heart failure.
Switch Between El Nino and La Nina is Caused by Subsurface Ocean Waves Likely Driven by Lunar Tidal Forcing
Authors: Lin Jialin , Qian Taotao 
Published: September 2019

AbstractThe El Nino-Southern Oscillation (ENSO) is the dominant interannual variability of Earth’s climate system, and strongly modulates global temperature, precipitation, atmospheric circulation, tropical cyclones and other extreme events. However, forecasting ENSO is one of the most difficult problems in climate sciences affecting both interannual climate prediction and decadal prediction of near-term global climate change. The key question is what cause the switch between El Nino and La Nina. For the past 30 years, ENSO forecasts have been limited to short lead times after ENSO sea surface temperature (SST) anomaly has already developed, but unable to predict the switch between El Nino and La Nina. Here, we demonstrate that the switch between El Nino and La Nina is caused by a subsurface ocean wave propagating from western Pacific to central and eastern Pacific and then triggering development of SST anomaly. This is based on analysis of all ENSO events in the past 136 years using multiple long-term observational datasets. The wave’s slow phase speed and decoupling from atmosphere indicate that it is a forced wave. Further analysis of Earth’s angular momentum budget and NASA’s Apollo Landing Mirror Experiment suggests that the subsurface wave is likely driven by lunar tidal gravitational force.
New crosstalk between probiotics Lactobacillus plantarum and Bacillus subtilis
Authors: Yu Tao , Kong Jian , Zhang Li , Gu Xinyi , Wang Mingyu , Guo Tingting 
Published: September 2019

AbstractIt was reported that oral administration of Bacillus favored the growth of Lactobacillus in the intestinal tract. Here, this phenomenon was confirmed by co-cultivation of Bacillus subtilis 168 and Lactobacillus plantarum SDMCC050204-pL157 in vitro. To explain the possible molecular mechanisms, B. subtilis 168 cells were incubated in simulated intestinal fluid at 37 °C for 24 h, and up to 90% of cells autolysed in the presence of bile salts. Addition of the autolysate to medium inoculated with Lb. plantarum SDMCC050204 decreased the concentration of H2O2 in the culture, alleviated DNA damage and increased the survival of Lb. plantarum, as like the results of exogenous heme addition. These results suggested that the autolysate provided heme, which activated the heme-dependent catalase KatA in Lb. plantarum SDMCC050204. HPLC confirmed the presence of heme in the autolysate. Disruption of the Lb. plantarum SDMCC050204 katA gene abolished the protective effect of the B. subtilis 168 autolysate against H2O2 stress. We thus hypothesized that the beneficial effect of Bacillus toward Lactobacillus was established through activation of the heme-dependent catalase and remission of the damage of reactive oxygen species against Lactobacillus. This study raised new crosstalk between the two frequently-used probiotics, highlighting heme-dependent catalase as the key mediator.
The involvement of McpB chemoreceptor from Pseudomonas aeruginosa PAO1 in virulence
Authors: García-Fontana Cristina , Vílchez Juan I. , González-Requena Marta , González-López Jesús , Krell Tino , Matilla Miguel A. , Manzanera Maximino 
Published: September 2019

AbstractPseudomonas aeruginosa is an opportunistic human pathogen causing infections in a variety of plant and animal hosts. The gene mcpB, part of the chemosensory gene cluster II, encodes a soluble chemoreceptor whose function remains unknown. Previous studies show that the cheB2 gene, also located in the chemosensory cluster II, is involved in a specific response during infection and it is required for full pathogenicity of P. aeruginosa. To determine whether the McpB (or Aer2) chemoreceptor is involved in virulence processes, we generated a mcpB mutant and tested its phenotype using a virulence-measuring system. This system was developed by our group and is based on different bioassays using organisms living at different soil trophic levels, including microbial, nematode, arthropod, annelid, and plant model systems. The deletion of mcpB resulted in an attenuation of bacterial virulence in different infection models, and wild-type virulence was restored following genetic complementation of the mutant strain. Our study indicates that the McpB chemoreceptor is linked to virulence processes and may constitute the basis for the development of alternative strategies against this pathogen.
The Secretomes of Painful Versus Nonpainful Human Schwannomatosis Tumor Cells Differentially Influence Sensory Neuron Gene Expression and Sensitivity
Authors: Ostrow Kimberly Laskie , Donaldson Katelyn J. , Caterina Michael J. , Belzberg Allan , Hoke Ahmet 
Published: September 2019

AbstractSchwannomatosis is a multiple tumor syndrome in which patients develop benign tumors along peripheral nerves throughout the body. The first symptom with which schwannomatosis patients often present, prior to discovery of tumors, is pain. This pain can be debilitating and is often inadequately alleviated by pharmacological approaches. Schwannomatosis-associated pain can be localized to the area of a tumor, or widespread. Moreover, not all tumors are painful, and the occurrence of pain is often unrelated to tumor size or location. We speculate that some individual tumors, but not others, secrete factors that act on nearby nerves to augment nociception by producing neuronal sensitization or spontaneous neuronal firing. We created cell lines from human SWN tumors with varying degrees of pain. We have found that conditioned medium (CM) collected from painful SWN tumors, but not that from nonpainful SWN tumors, sensitized DRG neurons, causing increased sensitivity to depolarization by KCl, increased response to noxious TRPV1 and TRPA1 agonists and also upregulated the expression of pain-associated genes in DRG cultures. Multiple cytokines were also detected at higher levels in CM from painful tumors. Taken together our data demonstrate a differential ability of painful versus non-painful human schwannomatosis tumor cells to secrete factors that augment sensory neuron responsiveness, and thus identify a potential determinant of pain heterogeneity in schwannomatosis.