bluuebunny/crossref_metadata_2025 huggingface dataset:
The physics of tossing fried rice
Authors: Ko Hungtang , Hu David L.
Published: February 2020

Fried rice is a 1500-year-old dish that is prepared using wok tossing, a technique that enables food to undergo temperatures of 1200°C without burning. Tossing of the heavy wok at high speed may be one contributor to shoulder pain, which is reported by 64.5% of Chinese restaurant chefs. In this combined experimental and theoretical study, we report the wok tossing kinematics of five professional restaurant chefs. The wok toss has a period of 0.3 s and involves two directions of movement: translation, which slides the rice along the wok, and rotation, which throws the rice into the air. We report the chosen kinematics of the chefs and use a theoretical model to predict the trajectory of rice based on projectile motion. Using our model, we rank all possible kinematics in terms of three metrics: the proportion of the rice that is tossed, its flight height and the angular displacement of the rice. We identify an optimal regime for making fried rice and suggest ways that wok tossing may be improved. This study may inspire the design of stir-fry robotics and exoskeletons to reduce the rate of muscle strain injury among professional chefs.
Disentangling the behavioural variability of confined cell migration
Authors: Brückner David B. , Fink Alexandra , Rädler Joachim O. , Broedersz Chase P.
Published: February 2020

Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows under identical conditions. Here, we observe the migration of single human breast cancer cells (MDA-MB-231) in confining two-state micropatterns. To describe the stochastic dynamics of this confined migration, we employ a dynamical systems approach. We identify statistics to measure the behavioural variance of the migration, which significantly exceeds that predicted by a population-averaged stochastic model. This additional variance can be explained by the combination of an ‘ageing’ process and population heterogeneity. To quantify population heterogeneity, we decompose the cells into subpopulations of slow and fast cells, revealing the presence of distinct classes of dynamical systems describing the migration, ranging from bistable to limit cycle behaviour. Our findings highlight the breadth of migration behaviours present in cell populations.
A platform for light-controlled formation of free-stranding lipid membranes
Authors: Ryzhkov Nikolay V. , Skorb Ekaterina V.
Published: February 2020

The engineering of artificial cells is one of the most significant scientific challenges. Thus, controlled fabrication and
in situ
monitoring of biomimetic nanoscale objects are among the central issues in current science and technology. Studies of transmembrane channels and cell mechanics often require the formation of lipid bilayers (LBs), their modification and their transfer to a particular place. We present here a novel approach for remotely controlled manipulation of LBs. Layer-by-layer deposition of polyethyleneimine and poly(sodium 4-styrenesulfonate) on a nanostructured TiO
2
photoanode was performed to obtain a surface with the desired net charge and to enhance photocatalytic performance. The LB was deposited on top of a multi-layer positive polymer cushion by the dispersion of negative vesicles. The separation distance between the electrostatically linked polyelectrolyte cushion and the LB can be adjusted by changing the environmental pH, as zwitter-ionic lipid molecules undergo pH-triggered charge-shifting. Protons were generated remotely by photoanodic water decomposition on the TiO
2
surface under 365 nm illumination. The resulting pH gradient was characterized by scanning vibrating electrode and scanning ion-selective electrode techniques. The light-induced reversible detachment of the LB from the polymer-cushioned photoactive substrate was found to correlate with suggested impedance models.
John Collins and the Double Horizontal Dial
Authors: Turner Anthony , Davis John
Published: February 2020

On his admission to the Royal Society in 1667, John Collins presented to it, and described, an example of Henry Sutton's double horizontal dial with additions by himself. His description given on that occasion is here transcribed with some commentary both on the dial itself and on Collins’ involvement with it.
Molecular anatomy of the pre-primitive-streak chick embryo
Authors: Lee Hyung Chul , Lu Hui-Chun , Turmaine Mark , Oliveira Nidia M. M. , Yang Youwen , De Almeida Irene , Stern Claudio D.
Published: February 2020

The early stages of development of the chick embryo, leading to primitive streak formation (the start of gastrulation), have received renewed attention recently, especially for studies of the mechanisms of large-scale cell movements and those that position the primitive streak in the radial blastodisc. Over the long history of chick embryology, the terminology used to define different regions has been changing, making it difficult to relate studies to each other. To resolve this objectively requires precise definitions of the regions based on anatomical and functional criteria, along with a systematic molecular map that can be compared directly to the functional anatomy. Here, we undertake these tasks. We describe the characteristic cell morphologies (using scanning electron microscopy and immunocytochemistry for cell polarity markers) in different regions and at successive stages. RNAseq was performed for 12 regions of the blastodisc, from which a set of putative regional markers was selected. These were studied in detail byin situhybridization. Together this provides a comprehensive resource allowing the community to define the regions unambiguously and objectively. In addition to helping with future experimental design and interpretation, this resource will also be useful for evolutionary comparisons between different vertebrate species.
Cultural prerequisites of socioeconomic development
Authors: Ruck Damian J. , Bentley R. Alexander , Lawson Daniel J.
Published: February 2020

In the centuries since the enlightenment, the world has seen an increase in socioeconomic development, measured as increased life expectancy, education, economic development and democracy. While the co-occurrence of these features among nations is well documented, little is known about their origins or co-evolution. Here, we compare this growth of prosperity in nations to the historical record of cultural values in the twentieth century, derived from global survey data. We find that two cultural factors, secular-rationality and cosmopolitanism, predict future increases in GDPper capita, democratization and secondary education enrollment. The converse is not true, however, which indicates that secular-rationality and cosmopolitanism are among the preconditions for socioeconomic development to emerge.
Effect of storage condition on the physico-chemical properties of corn–wheat starch/zein edible bilayer films
Authors: Chen Chen , Du Yan , Zuo Guanjie , Chen Fusheng , Liu Kunlun , Zhang Lifen
Published: February 2020

The functional properties of biopolymer-based film packaging materials are susceptible to external storage conditions. The effects of different storage temperature, relative humidity (RH) and duration on the apparent form, barrier properties, mechanical properties and microstructure of corn–wheat starch/zein bilayer films were studied. From 0 to 150 days, storage temperature and RH, but not storage time, affected the appearance and colour of the bilayer films. The increase in haze of the bilayer films stored at 25°C was much greater than that at low temperatures. With increased storage time, the moisture content first increased and then decreased, while the water resistance and oxygen barrier properties of the bilayer films worsened. After 150 days, the bilayer film stored at 25°C with 54% RH had better water resistance properties. The oxygen barrier properties of the bilayer film stored at 25°C with 43% RH were preferable to those of other groups because the peroxide value of vegetable oil packed in the former bilayer film was the lowest. The tensile strength of bilayer films stored at 25°C with RH of 43, 54 and 65% decreased, but was still better than those stored at low temperatures (−17°C, 4°C), which were tough due to their high elongation at break. Scanning electron microscopy results showed tight bonds between the bilayer films, and the network structure inside the films disappeared and reappeared during storage. The cross-sectional compactness changed, and there was no film separation after 150 days.
Commodity-specific punishment for experimentally induced defection in cooperatively breeding fish
Authors: Naef Jan , Taborsky Michael
Published: February 2020

Coercion is an important but underrated component in the evolution of cooperative behaviour. According to the pay-to-stay hypothesis of cooperative breeding, subordinates trade alloparental care for the concession to stay in the group. Punishment of idle subordinates is a key prediction of this hypothesis, which has received some experimental scrutiny. However, previous studies neither allowed separating between punishment and effects of disruption of social dynamics, nor did they differentiate between different helping behaviours that may reflect either mutualistic or reciprocal interaction dynamics. In the cooperative breeder
Neolamprologus pulcher
, we experimentally engineered the ability of subordinates to contribute to alloparental care by manipulating two different helping behaviours independently from one another in a full factorial design. We recorded the treatment effects on breeder aggression, subordinate helping efforts and submissive displays. We found two divergent regulatory mechanisms of cooperation, dependent on behavioural function. Experimental impediment of territory maintenance of subordinates triggered punishment by dominants, whereas prevented defence against egg predators released a compensatory response of subordinates without any enforcement, suggesting pre-emptive appeasement. These effects occurred independently of one another. Apparently, in the complex negotiation process among members of cooperative groups, behaviours fulfilling different functions may be regulated by divergent interaction mechanisms.
Long-term consistency of personality traits of cattle
Authors: Neave Heather W. , Costa Joao H. C. , Weary Daniel M. , von Keyserlingk Marina A. G.
Published: February 2020

Personality is often defined as the behaviour of individual animals that is consistent across contexts and over time. Personality traits may become unstable during stages of ontogeny from infancy to adulthood, especially during major periods of development such as around the time of sexual maturation. The personality of domesticated farm animals has links with productivity, health and welfare, but to our knowledge, no studies have investigated the development and stability of personality traits across developmental life stages in a mammalian farm animal species. Here, we describe the consistency of personality traits across ontogeny in dairy cattle from neonate to first lactation as an adult. The personality traits ‘bold’ and ‘exploratory’, as measured by behavioural responses to novelty, were highly consistent during the earlier (before and after weaning from milk) and later (after puberty to first lactation) rearing periods, but were not consistent across these rearing periods when puberty occurred. These findings indicate that personality changes in cattle around sexual maturation are probably owing to major physiological changes that are accelerated under typical management conditions at this time. This work contributes to the understanding of the ontogeny of behaviour in farm animals, especially how and why individuals differ in their behaviour.
Early Oligocene chinchilloid caviomorphs from Puerto Rico and the initial rodent colonization of the West Indies
Authors: Marivaux Laurent , Vélez-Juarbe Jorge , Merzeraud Gilles , Pujos François , Viñola López Lázaro W. , Boivin Myriam , Santos-Mercado Hernán , Cruz Eduardo J. , Grajales Alexandra , Padilla James , Vélez-Rosado Kevin I. , Philippon Mélody , Léticée Jean-Len , Münch Philippe , Antoine Pierre-Olivier
Published: February 2020

By their past and present diversity, rodents are among the richest components of Caribbean land mammals. Many of these became extinct recently. Causes of their extirpation, their phylogenetic affinities, the timing of their arrival in the West Indies and their biogeographic history are all ongoing debated issues. Here, we report the discovery of dental remains from Lower Oligocene deposits (ca29.5 Ma) of Puerto Rico. Their morphology attests to the presence of two distinct species of chinchilloid caviomorphs, closely related to dinomyids in a phylogenetic analysis, and thus of undisputable South American origin. These fossils represent the earliest Caribbean rodents known thus far. They could extend back to 30 Ma the lineages of some recently extinct Caribbean giant rodents (ElasmodontomysandAmblyrhiza), which are also retrieved here as chinchilloids. This new find has substantial biogeographic implications because it demonstrates an early dispersal of land mammals from South America to the West Indies, perhaps via the emergence of the Aves Ridge that occurredca35–33 Ma (GAARlandia hypothesis). Considering both this new palaeontological evidence and recent molecular divergence estimates, the natural colonization of the West Indies by rodents probably occurred through multiple and time-staggered dispersal events (chinchilloids, then echimyid octodontoids (spiny rats/hutias), caviids and lastly oryzomyin muroids (rice rats)).
Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant
Authors: Qin Dan , Ma Cong , Lv Min , Yu Chang-Ping
Published: February 2020

Two Gram-stain-negative, aerobic, motile and rod-shaped bacteria, one designated as strain AXBT, capable of degrading estrogens, and another, YL23T, capable of degrading estrogen and bisphenol A, were isolated from activated sludge in Xiamen City, PR China. The optimum temperature and pH of both strains were 25–35 °C and pH 7.0–8.0. While strain AXBT could tolerate 3 % (w/v) NaCl, YL23T could only grow between 0–1 % (w/v) NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c) as the major fatty acids and diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G+C contents of strains AXBT and YL23T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXBT and YL23T belonged to the genus

Sphingobium

. Strain AXBT was most closely related to

Sphingobium chlorophenolicum

NBRC 16172T (97.5 %) and

Sphingobium chungbukense

DJ77T (97.2 %), and strain YL23T was most closely related to

S. chlorophenolicum

NBRC 16172T (97.4 %) and

S. quisquiliarum

P25T (97.1 %). Average nucleotide identity values between these two strains and

S. chlorophenolicum

NBRC 16172T,

S. chungbukense

DJ77T,

Sphingobium chinhatense

IP26T,

Sphingobium quisquiliarum

P25T and

Sphingobium japonicum

UT26ST were from 80.7 to 85.8 %. In conclusion, strains AXBT and YL23T represent novel species of the genus

Sphingobium

, for which the names Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov. are proposed, respectively. The type strains of S. estronivorans and S. bisphenolivorans are AXBT (=MCCC 1K01232T=DSM 102173T) and YL23T (=MCCC 1K02300T=DSM 102172T), respectively.
The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19
Authors: Sarkar Bishajit , Ullah Md. Asad , Johora Fatema Tuz , Taniya Masuma Afrin , Araf Yusha
Published: February 2020

Wuhan Novel Coronavirus disease (COVID-19) outbreak has become a global outbreak which has raised the concern of scientific community to design and discover a definitive cure against this deadly virus which has caused deaths of numerous infected people upon infection and spreading. To date, no antiviral therapy or vaccine is available which can effectively combat the infection caused by this virus. This study was conducted to design possible epitope-based subunit vaccines against the SARS-CoV-2 virus using the approaches of reverse vaccinology and immunoinformatics. Upon continual computational experimentation three possible vaccine constructs were designed and one vaccine construct was selected as the best vaccine based on molecular docking study which is supposed to effectively act against SARS-CoV-2. Later, molecular dynamics simulation and in silico codon adaptation experiments were carried out in order to check biological stability and find effective mass production strategy of the selected vaccine. Hopefully, this study will contribute to uphold the present efforts of the researches to secure a definitive treatment against this lethal virus.
The Pathogenicity of SARS-CoV-2 in hACE2 Transgenic Mice
Authors: Bao Linlin , Deng Wei , Huang Baoying , Gao Hong , Liu Jiangning , Ren Lili , Wei Qiang , Yu Pin , Xu Yanfeng , Qi Feifei , Qu Yajin , Li Fengdi , Lv Qi , Wang Wenling , Xue Jing , Gong Shuran , Liu Mingya , Wang Guanpeng , Wang Shunyi , Song Zhiqi , Zhao Linna , Liu Peipei , Zhao Li , Ye Fei , Wang Huijuan , Zhou Weimin , Zhu Na , Zhen Wei , Yu Haisheng , Zhang Xiaojuan , Guo Li , Chen Lan , Wang Conghui , Wang Ying , Wang Xinming , Xiao Yan , Sun Qiangming , Liu Hongqi , Zhu Fanli , Ma Chunxia , Yan Lingmei , Yang Mengli , Han Jun , Xu Wenbo , Tan Wenjie , Peng Xiaozhong , Jin Qi , Wu Guizhen , Qin Chuan
Published: February 2020

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) caused the Corona Virus Disease 2019 (COVID-19) cases in China has become a public health emergency of international concern (PHEIC). Based on angiotensin converting enzyme 2 (ACE2) as cell entry receptor of SARS-CoV, we used the hACE2 transgenic mice infected with SARS-CoV-2 to study the pathogenicity of the virus. Weight loss and virus replication in lung were observed in hACE2 mice infected with SARS-CoV-2. The typical histopathology was interstitial pneumonia with infiltration of significant lymphocytes and monocytes in alveolar interstitium, and accumulation of macrophages in alveolar cavities. Viral antigens were observed in the bronchial epithelial cells, alveolar macrophages and alveolar epithelia. The phenomenon was not found in wild type mice with SARS-CoV-2 infection. The pathogenicity of SARS-CoV-2 in hACE2 mice was clarified and the Koch’s postulates were fulfilled as well, and the mouse model may facilitate the development of therapeutics and vaccines against SARS-CoV-2.
Neutrophil-to-Lymphocyte Ratio Predicts Severe Illness Patients with 2019 Novel Coronavirus in the Early Stage
Authors: Liu Jingyuan , Liu Yao , Xiang Pan , Pu Lin , Xiong Haofeng , Li Chuansheng , Zhang Ming , Tan Jianbo , Xu Yanli , Song Rui , Song Meihua , Wang Lin , Zhang Wei , Han Bing , Yang Li , Wang Xiaojing , Zhou Guiqin , Zhang Ting , Li Ben , Wang Yanbin , Chen Zhihai , Wang Xianbo
Published: February 2020

Background

Severe ill patients with 2019 novel coronavirus (2019-nCoV) infection progressed rapidly to acute respiratory failure. We aimed to select the most useful prognostic factor for severe illness incidence.

Methods

The study prospectively included 61 patients with 2019-nCoV infection treated at Beijing Ditan Hospital from January 13, 2020 to January 31, 2020. Prognostic factor of severe illness was selected by the LASSO COX regression analyses, to predict the severe illness probability of 2019-CoV pneumonia. The predictive accuracy was evaluated by concordance index, calibration curve, decision curve and clinical impact curve.

Results

The neutrophil-to-lymphocyte ratio (NLR) was identified as the independent risk factor for severe illness in patients with 2019-nCoV infection. The NLR had a c-index of 0.807 (95% confidence interval, 0.676–0.38), the calibration curves fitted well, and the decision curve and clinical impact curve showed that the NLR had superior standardized net benefit. In addition, the incidence of severe illness was 9.1% in age ≥ 50 and NLR < 3.13 patients, and half of patients with age ≥ 50 and NLR ≥ 3.13 would develop severe illness. Based on the risk stratification of NLR with age, the study developed a 2019-nCoV pneumonia management process.

Conclusions

The NLR was the early identification of risk factors for 2019-nCoV severe illness. Patients with age ≥ 50 and NLR ≥ 3.13 facilitated severe illness, and they should rapidly access to intensive care unit if necessary.
Isolevuglandins promote autoimmunity and hypertension in systemic lupus erythematosus
Authors: Patrick David M. , de la Visitación Nestor , Ormseth Michelle J. , Stein C. Michael , Davies Sean S. , Yermalitksy Valery N. , Amarnath Venkataraman , Crofford Leslie J. , Williams Jonathan M. , Dikalov Sergey , Dikalova Anna , Xiao Liang , Van Beusecum Justin P. , Ao Mingfang , Fogo Agnes B. , Kirabo Annet , Harrison David G.
Published: February 2020

Hypertension, vascular inflammation and renal inflammation are characteristic of systemic lupus erythematosus (SLE), a multisystem autoimmune disease that is complex and poorly understood. Oxidation products of arachidonic and other fatty acids, termed isolevuglandins (isoLG) lead to formation of post-translational protein modifications that are immunogenic. We demonstrate isoLG enrichment in dendritic cells (DCs), B cells, and plasma cells from juvenile femaleB6.SLE123mice. In adultB6.SLE123andNZBWF1mice, isoLG adducts are enriched in plasma cells and splenic DCs compared toC57Bl/6andNZWmice respectively. Treatment with the isoLG-scavenger 2-hydroxybenzylamine (2-HOBA) reduced blood pressure, improved renal function, and attenuated renal injury. Moreover, 2-HOBA reduced bone marrow plasma cells, total IgG levels, and anti-dsDNA antibody titers. We also demonstrate that mice with SLE generate specific IgG antibodies against isoLG adducted protein, confirming the immunogenicity of isoLG adducts. Finally, we found that isoLG adducted peptides are markedly enriched in monocytes from patients with SLE which was accompanied by an increase in superoxide production. These findings support a role of isoLG adducts in the genesis and maintenance of systemic autoimmunity and its associated hypertension in SLE. Scavenging of isoLGs promises to be a novel therapy for this disease.
Metabolomic changes associated with frontotemporal lobar degeneration syndromes
Authors: Murley Alexander G. , Jones P Simon , Gilchrist Ian Coyle , Bowns Lucy , Wiggins Julie , Tsvetanov Kamen A. , Rowe James B.
Published: February 2020

Objective

Widespread metabolic changes are seen in neurodegenerative disease and could be used as biomarkers for diagnosis and disease monitoring. They may also reveal disease mechanisms that could be a target for therapy. In this study we looked for blood-based biomarkers in syndromes associated with frontotemporal lobar degeneration.

Methods

Plasma metabolomic profiles were measured from 134 patients with frontotemporal lobar degeneration (behavioural variant frontotemporal dementia n=30, non fluent variant primary progressive aphasia n=26, progressive supranuclear palsy n=45, corticobasal syndrome n=33) and 32 healthy controls.

Results

Forty-nine of 842 metabolites were significantly altered in frontotemporal lobar degeneration (after false-discovery rate correction for multiple comparisons). These were distributed across a wide range of metabolic pathways including amino acids, energy and carbohydrate, cofactor and vitamin, lipid and nucleotide pathways. The metabolomic profile supported classification between frontotemporal lobar degeneration and controls with high accuracy (88.1-96.6%) while classification accuracy was lower between the frontotemporal lobar degeneration syndromes (72.1-83.3%). One metabolic profile, comprising a range of different pathways, was consistently identified as a feature of each disease versus controls: the degree to which a patient expressed this metabolomic profile was associated with their subsequent survival (hazard ratio 0.74 [0.59-0.93], p = 0.0018).

Conclusions

The metabolic changes in FTLD are promising diagnostic and prognostic biomarkers. Further work is required to replicate these findings, examine longitudinal change, and test their utility in differentiating between FTLD syndromes that are pathologically distinct but phenotypically similar.
Statistical Inference for Coronavirus Infected Patients in Wuhan
Authors: Zhou Yong-Dao , Dong Jianghu James
Published: February 2020

Importance

The new coronavirus outbreak has seriously affected the quality of life in China. Wuhan is the disaster area, where the number of cases has increased rapidly. However, the current measures of infected patients in Wuhan are still underestimated.

Objective

To estimate the overall infected patients in Wuhan from several sampled data. The correct estimated infected patients can be helpful for the government to arrange the needed beds in hospital wards to meet the actual needs.

Design

We proposed to use the sampling survey to estimate the overall infected patients in Wuhan. The sampling survey is a kind of non-comprehensive survey. It selected some units from all the survey objects to carry out the survey and made the estimation and inference to all the survey objects. Sampling surveys can obtain information that reflects the overall situation, although it is not a comprehensive survey.

Setting

We estimated the overall infection rate in Wenzhou city, which has a better data collection system. Simultaneously, another different samples of Wuhan tourists to Singapore will be used to validate the infection rate in Wenzhou city. Combined these two samples, we give the estimation of the number of infected patients in Wuhan and other prefecture-level cities in Hubei Province.

Participants

The number of people who returned from Wuhan to Wenzhou was selected from the daily notification of the pneumonia epidemic caused by a new coronavirus infection in the city.

Exposures for observational studies

The daily rate of the pneumonia epidemic caused by the new coronavirus infection in Wenzhou City. The numerator is the number of people diagnosed and whether each person diagnosed had a history of living in Wuhan. The denominator is the total number of people returning to Wenzhou from Wuhan. Based on this rate, it is reasonable to predict the number of the infected patients.

Main Outcome(s) and Measure(s)

According to the most conservative estimate from our proposed sampling method, at least total 54,000 infected patients are in Wuhan. Therefore, the current 8,000 beds in hospital wards and the 20,000 beds in square-class hospitals are far away from meeting the actual needs.
Distribution of the 2019-nCoV Epidemic and Correlation with Population Emigration from Wuhan, China
Authors: Chen Zeliang , Zhang Qi , Lu Yi , Guo Zhongmin , Zhang Xi , Zhang Wenjun , Guo Cheng , Liao Conghui , Li Qianlin , Han Xiaohu , Lu Jiahai
Published: February 2020

BACKGROUNDS

The ongoing new coronavirus (2019-nCoV) pneumonia outbreak is spreading in China and has not reached its peak. Five millions of people had emigrated from Wuhan before the city lockdown, which potentially represent a source of virus spreaders. Case distribution and its correlation with population emigration from Wuhan in early epidemic are of great importance for early warning and prevention of future outbreak.

METHODS

The officially reported cases of 2019-nCoV pneumonia were collected as of January 30, 2020. Time and location information of these cases were extracted analyzed with ArcGIS and WinBUGS. Population migration data of Wuhan City and Hubei province were extracted from Baidu Qianxi and analyzed for their correlation with case number.

FINDINGS

The 2019-nCoV pneumonia cases were predominantly distributed in Hubei and other provinces of South China. Hot spot provinces included Sichuan and Yunnan provinces that are adjacent to Hubei. While Wuhan city has the highest number of cases, the time risk is relatively stable. Numbers of cases in some cities are relatively low, but the time risks are continuously rising. The case numbers of different provinces and cities of Hubei province were highly correlated with the emigrated populations from Wuhan. Lockdown of 19 cities of Hubei province, and implementation of nationwide control measures efficiently prevented the exponential growth of case number.

INTERPRETATION

Population emigrated from Wuhan was the main infection source for other cities and provinces. Some cities with low case number but were in rapid increase. Due to the upcoming Spring Festival return transport wave, understanding of the trends of risks in different regions is of great significance for preparedness for both individuals and institutions.

FUNDINGS

National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, State Key Program of National Natural Science of China.
Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers
Authors: Thiecke Michiel J. , Wutz Gordana , Muhar Matthias , Tang Wen , Bevan Stephen , Malysheva Valeriya , Stocsits Roman , Neumann Tobias , Zuber Johannes , Fraser Peter , Schoenfelder Stefan , Peters Jan-Michael , Spivakov Mikhail
Published: February 2020

It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows that steady-state transcription of only a minority of genes is affected by depletion of architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics of chromosomal contacts of all human gene promoters upon rapid architectural protein degradation. We show that promoter contacts lost in these conditions tend to be long-range, with at least one interaction partner localising in the vicinity of topologically associated domain (TAD) boundaries. In contrast, many shorter-range chromosomal contacts, particularly those that connect active promoters with each other and with active enhancers remain unaffected by cohesin and CTCF depletion. We demonstrate that the effects of cohesin depletion on nascent transcription can be explained by changes in the connectivity of their enhancers. Jointly, these results provide a mechanistic explanation to the limited, but consistent effects of cohesin and CTCF on steady-state transcription and point towards the existence of alternative enhancer-promoter pairing mechanisms that are independent of these proteins.
Rpgrip1l controls ciliary gating by ensuring the proper amount of Cep290 at the vertebrate transition zone
Authors: Wiegering Antonia , Dildrop Renate , Vesque Christine , Schneider-Maunoury Sylvie , Gerhardt Christoph
Published: February 2020

A range of severe human diseases called ciliopathies are caused by the dysfunction of primary cilia. Primary cilia are cytoplasmic protrusions consisting of the basal body (BB), the axoneme and the transition zone (TZ). The BB is a modified mother centriole from which the axoneme, the microtubule-based ciliary scaffold, is formed. At the proximal end of the axoneme, the TZ functions as the ciliary gate governing ciliary protein entry and exit. Since ciliopathies often develop due to mutations in genes encoding proteins that localise to the TZ, the understanding of the mechanisms underlying TZ function is of eminent importance. Here, we show that the ciliopathy protein Rpgrip1l governs ciliary gating by ensuring the proper amount of Cep290 at the vertebrate TZ. Further, we identified the flavonoid eupatilin as a potential agent to tackle ciliopathies caused by mutations inRPGRIP1Las it rescues ciliary gating in the absence of Rpgrip1l.
Modeling How Community Assembly Alters the Functioning of Ecosystems
Authors: Koffel Thomas , Kremer Colin T , Bannar-Martin K. , Ernest S.K. Morgan , Eisenhauer Nico , Roscher Christiane , Cabral Juliano Sarmento , Leibold Mathew A.
Published: February 2020

Although the effects of species richness on ecosystem functioning have been extensively studied, there is increased interest in understanding how community assembly in general might alter the functioning of ecosystems. We focus on two complementary approaches for evaluating how community assembly influences ecosystem function (here, productivity). The first quantifies the relative importance of complementarity and selection by contrasting monocultures with polycultures. The second identifies the effects of species losses and/or gains relative to the baseline polyculture, as well as the indirect effects on other species’ productivity. We evaluate and contrast these two approaches, using simulated communities structured by different, known competition mechanisms, where species compete for different resources and experience varying levels of environmental heterogeneity. We find that the metrics provided by these approaches can jointly discriminate the mechanisms of competition driving productivity. We then apply our methods to data from a long-term biodiversity-ecosystem experiment (the Jena Experiment) and find that the data do not correspond to any of the competition scenarios we modeled. We address two additional possible complications: facilitation by nitrogen fixing plants, and non-equilibrium behavior during community assembly, and find that a combination of resource competition and facilitation by nitrogen fixing plants is the more likely explanation for the results obtained at Jena.
Spatial Distribution of Discarded Vehicle Tires and Their Influence onAedes albopictusandCulex quinquefasciatusPopulations, New Orleans, Louisiana
Authors: Sallam Mohamed F. , Ahmed Tamer , Sylvain-Lear Cynthia , Riegel Claudia , Moise Imelda K.
Published: February 2020

Discarded vehicle tires play an important role in the colonization of container mosquito populations, particularly their geographic expansion. We assessed the spatial distribution of illegally discarded tires and their response to land use-land cover (LULC), and demographic factors using geospatial analysis and generalized regression. Multiple stepwise regressions were used to evaluate the response of the Container Index (CI) of colonizedAedes albopictus(Skuse), andCulex quinquefasciatusSay to macro- and microhabitats variables. The illegally discarded tires were distributed over 11 planning districts with clustering distribution for tires frequency and overdispersed distribution for tires number. Out of 1,137 (∼37.08%) water-holding tires, 598 (∼52.64%) tires at 65 (∼38.46%) sites were positive for colonized mosquito populations. A total of 13 mosquito species were identified, with the highest CI ofAe. albopictus(44.19%) andCx. quinquefasciatus(22.18%).Aedes albopictuscolonized all 65 sample sites andCx. quinquefasciatusfound at 32 sites. The Container Index (CI) of colonized mosquito was clustered in seven planning districts forAe. albopictusand five planning districts forCx. quinquefasciatus. Microhabitat (muddy water) rather than macrohabitats variables predicted both species’ colonization, especiallyAe. albopictus. The contribution of macro- and microhabitat characteristics in predicting colonized mosquito in water-holding tires was discussed.
Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation
Authors: Bertò Giulia , Bullock Daniel , Astolfi Pietro , Hayashi Soichi , Zigiotto Luca , Annicchiarico Luciano , Corsini Francesco , Benedictis Alessandro De , Sarubbo Silvio , Pestilli Franco , Avesani Paolo , Olivetti Emanuele
Published: February 2020

Virtual delineation of white matter bundles in the human brain is of paramount importance for multiple applications, such as pre-surgical planning and connectomics. A substantial body of literature is related to methods that automatically segment bundles from diffusion Magnetic Resonance Imaging (dMRI) data indirectly, by exploiting either the idea of connectivity between regions or the geometry of fiber paths obtained with tractography techniques, or, directly, through the information in volumetric data. Despite the remarkable improvement in automatic segmentation methods over the years, their segmentation quality is not yet satisfactory, especially when dealing with datasets with very diverse characteristics, such as different tracking methods, bundle sizes or data quality. In this work, we propose a novel, supervised streamline-based segmentation method, called Classifyber, which combines information from atlases, connectivity patterns, and the geometry of fiber paths into a simple linear model. With a wide range of experiments on multiple datasets that span from research to clinical domains, we show that Classifyber substantially improves the quality of segmentation as compared to other state-of-the-art methods and, more importantly, that it is robust across very diverse settings. We provide an implementation of the proposed method as open source code, as well as web service.
Evaluation of high-resolution atmospheric and oceanic simulations of the California Current System
Authors: Renault Lionel , McWilliams James C. , Kessouri Faycal , Jousse Alexandre , Frenzel Hartmut , Chen Ru , Deutsch Curtis
Published: February 2020

This paper is the first of two that present a 16-year hindcast solution from a coupled physical and biogeochemical model of the California Current System (CCS) along the U. S. West Coast and validate the physical solution with respect to mean, seasonal, interannual, and sub-seasonal fields and, to a lesser degree, eddy variability. Its companion paper is Deutsch et al. (2021a). The intent is to construct and demonstrate a modeling tool that will be used for mechanistic explanations, attributive causal assessments, and forecasts of future evolution for circulation and biogeochemistry, with particular attention to the increasing oceanic stratification, deoxygenation, and acidification. A well-resolved mesoscale (dx= 4 km) simulation of the CCS circulation is made with the Regional Oceanic Modeling System over a hindcast period of 16 years from 1995 to 2010. The oceanic solution is forced by a high-resolution (dx= 6 km) regional configuration of the Weather and Research Forecast (WRF) atmospheric model. Both of these high-resolution regional oceanic and atmospheric simulations are forced by lateral open boundary conditions taken from larger-domain, coarser-resolution parent simulations that themselves have boundary conditions from the Mercator and Climate Forecast System reanalyses, respectively. We show good agreement between the simulated atmospheric forcing of the oceanic and satellite measurements for the spatial patterns and temporal variability for the surface fluxes of momentum, heat, and freshwater. The simulated oceanic physical fields are then evaluated with satellite andin situmeasurements. The simulation reproduces the main structure of the climatological upwelling front and cross-shore isopycnal slopes, the mean current patterns (including the California Undercurrent), and the seasonal, interannual, and subseasonal variability. It also shows agreement between the mesoscale eddy activity and the windwork energy exchange between the ocean and atmosphere modulated by influences of surface current on surface stress. Finally, the impact of using a high frequency wind forcing is assessed for the importance of synoptic wind variability to realistically represent oceanic mesoscale activity and ageostrophic inertial currents.
Ultra-low DNA input into whole genome methylation assays and detection of oncogenic methylation & copy number variants in circulating tumour DNA
Authors: Whalley Celina , Payne Karl , Domingo Enric , Blake Andrew , Richman Susan , Brooks Jill , Batis Nikolaos , Spruce Rachel ,   S-CORT Consortium, Mehanna Hisham , Nankivell Paul , Beggs Andrew D
Published: February 2020

Background

CpG methylation in cancer is ubiquitous and generally detected in tumour specimens using a variety of techniques at a resolution encompassing single CpG loci to genome wide. Analysis of samples with very low DNA inputs, such as formalin fixed (FFPE) biopsy specimens from clinical trials or circulating tumour DNA has been challenging and has only been typically at single CpG sites. Analysis of genome wide methylation in these specimens has been limited because of the relative expense of techniques need to carry this out. We present the results of low input experiments into the Illumina Infinium HD methylation assay on FFPE specimens and ctDNA samples.

Methods

For all experiments, the Infinium HD assay for Methylation was used. In total, forty-eight FFPE specimens were used at varying concentrations (lowest input 50ng), eighteen blood derived specimens (lowest input 10ng) and six matched ctDNA input (lowest input 10ng) / fresh tumour specimens (lowest input 250ng) were processed. Downstream analysis was performed in R/Bioconductor for QC metrics and differential methylation analysis as well as copy number calls.

Results

Correlation coefficients for CpG methylation at the probe level averaged R2=0.99 for blood derived samples and R2>0.96 for the FFPE samples. When matched ctDNA/fresh tumour samples were compared R2>0.91. Results of differential methylation analysis did not vary significantly by DNA input in either the blood or FFPE groups. There were differences seen in the ctDNA group as compared to their paired tumour sample, possibly because of enrichment for tumour material without contaminating normal. Copy number variants observed in the tumour were generally also seen in the paired ctDNA sample.

Conclusions

The Illumina Infinium HD methylation assay can robustly detect methylation across a range of sample types, including ctDNA, down to a input of 10ng. It can also reliably detect oncogenic methylation changes and copy number variants in ctDNA.
Epidemiological and Clinical Characteristics of 17 Hospitalized Patients with 2019 Novel Coronavirus Infections Outside Wuhan, China
Authors: Li Jie , Li Shilin , Cai Yurui , Liu Qin , Li Xue , Zeng Zhaoping , Chu Yanpeng , Zhu Fangcheng , Zeng Fanxin
Published: February 2020

An increasing number of cases of novel coronavirus pneumonia (NCP) infected with 2019-nCoV have been identified in Wuhan and other cities in China, since December 2019. We analyzed data on the 17 confirmed cases in Dazhou to provide the epidemiologic characteristics of NCP outside Wuhan. Among them, 12 patients were still quarantined in the hospital, 5 patients were discharged NCP patients according to the national standards. Compared with non-discharged NCP patients, the discharged NCP patients had younger ages. Moreover, discharged NCP patients had higher heart rate, lymphocytes levels and monocytes levels than non-discharged NCP patients on admission to the hospital. Notably, all of 17 patients had abnormal increased C-reactive protein levels, and 16 patients had abnormal computed tomography images. This study provided some information that younger age, higher lymphocytes levels and monocytes levels at the diagnoses of 2019-nCoV may contributed to faster recovery and better therapeutic outcome.
Untangling biological factors influencing trajectory inference from single cell data
Authors: Charrout Mohammed , Reinders Marcel J.T. , Mahfouz Ahmed
Published: February 2020

Advances in single-cell RNA sequencing over the past decade has shifted the discussion of cell identity towards the transcriptional state of the cell. While the incredible resolution provided by single-cell RNA sequencing has led to great advances in unravelling tissue heterogeneity and inferring cell differentiation dynamics, it raises the question of which sources of variation are important for determining cellular identity. Here we show that confounding biological sources of variation, most notably the cell cycle, can distort the inference of differentiation trajectories. We show that by factorizing single cell data into distinct sources of variation, we can select a relevant set of factors that constitute the core regulators for trajetory inference, while filtering out confounding sources of variation (e.g. cell cycle) which can perturb the inferred trajectory. Script are available publicly onhttps://github.com/mochar/cell_variation.

Significance Statement

Pseudotime inference is a bioinformatics tool used to characterize and understand the role and activity of genes involved in cell differentiation. To achieve this, the level of expression of thousands of genes are simultaneously used to order cells along a developmental axis. However, this may result in distorted trajectories as many genes are not necessary involved in cell differentiation, and might even provide the pseudotime inference tool with conflicting (confounding) information. Here we present a methodology for improving inference of the differentiation trajectories by restricting it to a small set of genes assumed to regulate cell differentiation.
Paladin is a PI(4,5)P2phosphoinositide phosphatase that regulates endosomal signaling and angiogenesis
Authors: Nitzsche Anja , Pietilä Riikka , Testini Chiara , Ninchoji Takeshi , Smith Ross O. , Ekvärn Elisabet , Larsson Jimmy , Roche Francis P. , Egaña Isabel , Jauhiainen Suvi , Berger Philipp , Claesson-Welsh Lena , Hellström Mats
Published: February 2020

Cell signaling governs cellular behavior and is therefore subject to tight spatiotemporal regulation. Signaling output is regulated by specialized cell membranes and vesicles which contain unique combinations of lipids and proteins. The phospholipid phosphatidylinositol 4,5-bisphosphate, (PI(4,5)P2), an important component of the plasma membrane as well as other subcellular membranes, is involved in multiple processes, including signaling. However, which enzymes drive the formation and degradation of non-plasma membrane PI(4,5)P2, and their impact on cell signaling and function at the organismal level are unknown. Here we show in a mouse model that Paladin is a vascular PI(4,5)P2phosphatase that regulates endosomal signaling and angiogenesis. Paladin was localized to the endosomal and Golgi compartments, and interacted with vascular endothelial growth factor receptor 2 (VEGFR2)in vitroandin vivo. Loss of Paladin resulted in increased internalization of the receptor, over-activation of extracellular regulated kinase, and hypersprouting of endothelial cells in the developing retina of mice. These findings suggest that inhibition of Paladin, or other endosomal PI(4,5)P2phosphatases, could be exploited to modulate VEGFR2 signaling and angiogenesis, when direct and full inhibition of the receptor is not desirable.
mAML: an automated machine learning pipeline with a microbiome repository for human disease classification
Authors: Yang Fenglong , Zou Quan
Published: February 2020

Due to the concerted efforts to utilize the microbial features to improve disease prediction capabilities, automated machine learning (AutoML) systems designed to get rid of the tediousness in manually performing ML tasks are in great demand. Here we developed mAML, an ML model-building pipeline, which can automatically and rapidly generate optimized and interpretable models for personalized microbial classification tasks in a reproducible way. The pipeline is deployed on a web-based platform and the server is user-friendly, flexible, and has been designed to be scalable according to the specific requirements. This pipeline exhibits high performance for 13 benchmark datasets including both binary and multi-class classification tasks. In addition, to facilitate the application of mAML and expand the human disease-related microbiome learning repository, we developed GMrepo ML repository (GMrepo Microbiome Learning repository) from the GMrepo database. The repository involves 120 microbial classification tasks for 85 human-disease phenotypes referring to 12,429 metagenomic samples and 38,643 amplicon samples. The mAML pipeline and the GMrepo ML repository are expected to be important resources for researches in microbiology and algorithm developments.

Database URL

http://39.100.246.211:8050/Home