bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mean sea surface temperature changes influence ENSO-related precipitation changes in the mid-latitudes
Authors: Yang Young-Min , Park Jae-Heung , An Soon-Il , Wang Bin , Luo Xiao 
Published: March 2021

AbstractEl Niño profoundly impacts precipitation in high-population regions. This demands an advanced understanding of the changes in El Niño-induced precipitation under the future global warming scenario. However, thus far, consensus is lacking regarding future changes in mid-latitude precipitation influenced by El Niño. Here, by analyzing the Coupled Model Intercomparison Project simulations, we show that future precipitation changes are tightly linked to the response of each type of El Niño to the tropical Pacific mean sea surface temperature (SST) change. A La Niña-like mean SST change intensifies basin-wide El Niño events causing approximately 20% more precipitation over East Asia and North America via enhancing moisture transport. Meanwhile, an El Niño-like mean SST change generates more frequent eastern Pacific El Niño events, enhancing precipitation in North American. Our findings highlight the importance of the mean SST projection in selectively influencing the types of El Niño and their remote impact on precipitation.
Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE
Authors: He Jiangping , Babarinde Isaac A. , Sun Li , Xu Shuyang , Chen Ruhai , Shi Junjie , Wei Yuanjie , Li Yuhao , Ma Gang , Zhuang Qiang , Hutchins Andrew P. , Chen Jiekai 
Published: March 2021

AbstractTransposable elements (TEs) make up a majority of a typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity.
Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment
Authors: Stevenson Julia , Barrow-McGee Rachel , Yu Lu , Paul Angela , Mansfield David , Owen Julie , Woodman Natalie , Natrajan Rachael , Haider Syed , Gillett Cheryl , Tutt Andrew , Pinder Sarah E. , Choudary Jyoti , Naidoo Kalnisha 
Published: March 2021

AbstractIn breast cancer (BC), detecting low volumes of axillary lymph node (ALN) metastasis pre-operatively is difficult and novel biomarkers are needed. We recently showed that patient-derived ALNs can be sustained ex-vivo using normothermic perfusion. We now compare reactive (tumour-free;n = 5) and macrometastatic (containing tumour deposits >2 mm;n = 4) ALNs by combining whole section multiplex immunofluorescence with TMT-labelled LC-MS/MS of the circulating perfusate. Macrometastases contained significantly fewer B cells and T cells (CD4+/CD8+/regulatory) than reactive nodes (p = 0.02). Similarly, pathway analysis of the perfusate proteome (119/1453 proteins significantly differentially expressed) showed that immune function was diminished in macrometastases in favour of ‘extracellular matrix degradation’; only ‘neutrophil degranulation’ was preserved. Qualitative comparison of the perfusate proteome to that of node-positive pancreatic and prostatic adenocarcinoma also highlighted ‘neutrophil degranulation’ as a contributing factor to nodal metastasis. Thus, metastasis-induced changes in the REPLICANT perfusate proteome are detectable, and could facilitate biomarker discovery.
Dynamic control of the dopamine transporter in neurotransmission and homeostasis
Authors: Bu Mengfei , Farrer Matthew J. , Khoshbouei Habibeh 
Published: March 2021

AbstractThe dopamine transporter (DAT) transports extracellular dopamine into the intracellular space contributing to the regulation of dopamine neurotransmission. A reduction of DAT density is implicated in Parkinson’s disease (PD) by neuroimaging; dopamine turnover is dopamine turnover is elevated in early symptomatic PD and in presymptomatic individuals with monogenic mutations causal for parkinsonism. As an integral plasma membrane protein, DAT surface expression is dynamically regulated through endocytic trafficking, enabling flexible control of dopamine signaling in time and space, which in turn critically modulates movement, motivation and learning behavior. Yet the cellular machinery and functional implications of DAT trafficking remain enigmatic. In this review we summarize mechanisms governing DAT trafficking under normal physiological conditions and discuss how PD-linked mutations may disturb DAT homeostasis. We highlight the complexity of DAT trafficking and reveal DAT dysregulation as a common theme in genetic models of parkinsonism.
Gait speed in clinical and daily living assessments in Parkinson’s disease patients: performance versus capacity
Authors: Atrsaei Arash , Corrà Marta Francisca , Dadashi Farzin , Vila-Chã Nuno , Maia Luis , Mariani Benoit , Maetzler Walter , Aminian Kamiar 
Published: March 2021

AbstractGait speed often referred as the sixth vital sign is the most powerful biomarker of mobility. While a clinical setting allows the estimation of gait speed under controlled conditions that present functional capacity, gait speed in real-life conditions provides the actual performance of the patient. The goal of this study was to investigate objectively under what conditions during daily activities, patients perform as well as or better than in the clinic. To this end, we recruited 27 Parkinson’s disease (PD) patients and measured their gait speed by inertial measurement units through several walking tests in the clinic as well as their daily activities at home. By fitting a bimodal Gaussian model to their gait speed distribution, we found that on average, patients had similar modes in the clinic and during daily activities. Furthermore, we observed that the number of medication doses taken throughout the day had a moderate correlation with the difference between clinic and home. Performing a cycle-by-cycle analysis on gait speed during the home assessment, overall only about 3% of the strides had equal or greater gait speeds than the patients’ capacity in the clinic. These strides were during long walking bouts (>1 min) and happened before noon, around 26 min after medication intake, reaching their maximum occurrence probability 3 h after Levodopa intake. These results open the possibility of better control of medication intake in PD by considering both functional capacity and continuous monitoring of gait speed during real-life conditions.
Proximity to a critical point driven by electronic entropy in URu2Si2
Authors: Harrison Neil , Kushwaha Satya K. , Chan Mun K. , Jaime Marcelo 
Published: March 2021

AbstractThe strongly correlated actinide metal URu2Si2 exhibits a mean field-like second order phase transition at To ≈ 17 K, yet lacks definitive signatures of a broken symmetry. Meanwhile, various experiments have also shown the electronic energy gap to closely resemble that resulting from hybridization between conduction electron and 5f-electron states. We argue here, using thermodynamic measurements, that the above seemingly incompatible observations can be jointly understood by way of proximity to an entropy-driven critical point, in which the latent heat of a valence-type electronic instability is quenched by thermal excitations across a gap, driving the transition second order. Salient features of such a transition include a robust gap spanning highly degenerate features in the electronic density of states, that is weakly (if at all) suppressed by temperature on approaching To, and an elliptical phase boundary in magnetic field and temperature that is Pauli paramagnetically limited at its critical magnetic field.
TP63 basal cells are indispensable during endoderm differentiation into proximal airway cells on acellular lung scaffolds
Authors: Bilodeau Claudia , Shojaie Sharareh , Goltsis Olivia , Wang Jinxia , Luo Daochun , Ackerley Cameron , M Rogers Ian , Cox Brian , Post Martin 
Published: March 2021

AbstractThe use of decellularized whole-organ scaffolds for bioengineering of organs is a promising avenue to circumvent the shortage of donor organs for transplantation. However, recellularization of acellular scaffolds from multicellular organs like the lung with a variety of different cell types remains a challenge. Multipotent cells could be an ideal cell source for recellularization. Here we investigated the hierarchical differentiation process of multipotent ES-derived endoderm cells into proximal airway epithelial cells on acellular lung scaffolds. The first cells to emerge on the scaffolds were TP63+ cells, followed by TP63+/KRT5+ basal cells, and finally multi-ciliated and secretory airway epithelial cells. TP63+/KRT5+ basal cells on the scaffolds simultaneously expressed KRT14, like basal cells involved in airway repair after injury. Removal of TP63 by CRISPR/Cas9 in the ES cells halted basal and airway cell differentiation on the scaffolds. These findings suggest that differentiation of ES-derived endoderm cells into airway cells on decellularized lung scaffolds proceeds via TP63+ basal cell progenitors and tracks a regenerative repair pathway. Understanding the process of differentiation is key for choosing the cell source for repopulation of a decellularized organ scaffold. Our data support the use of airway basal cells for repopulating the airway side of an acellular lung scaffold.
A novel methodology for epidemic risk assessment of COVID-19 outbreak
Authors: Pluchino A. , Biondo A. E. , Giuffrida N. , Inturri G. , Latora V. , Le Moli R. , Rapisarda A. , Russo G. , Zappalà C. 
Published: March 2021

AbstractWe propose a novel data-driven framework for assessing the a-priori epidemic risk of a geographical area and for identifying high-risk areas within a country. Our risk index is evaluated as a function of three different components: the hazard of the disease, the exposure of the area and the vulnerability of its inhabitants. As an application, we discuss the case of COVID-19 outbreak in Italy. We characterize each of the twenty Italian regions by using available historical data on air pollution, human mobility, winter temperature, housing concentration, health care density, population size and age. We find that the epidemic risk is higher in some of the Northern regions with respect to Central and Southern Italy. The corresponding risk index shows correlations with the available official data on the number of infected individuals, patients in intensive care and deceased patients, and can help explaining why regions such as Lombardia, Emilia-Romagna, Piemonte and Veneto have suffered much more than the rest of the country. Although the COVID-19 outbreak started in both North (Lombardia) and Central Italy (Lazio) almost at the same time, when the first cases were officially certified at the beginning of 2020, the disease has spread faster and with heavier consequences in regions with higher epidemic risk. Our framework can be extended and tested on other epidemic data, such as those on seasonal flu, and applied to other countries. We also present a policy model connected with our methodology, which might help policy-makers to take informed decisions.
A randomized controlled trial on the effects induced by robot-assisted and usual-care rehabilitation on upper limb muscle synergies in post-stroke subjects
Authors: Lencioni T. , Fornia L. , Bowman T. , Marzegan A. , Caronni A. , Turolla A. , Jonsdottir J. , Carpinella I. , Ferrarin M. 
Published: March 2021

AbstractMuscle synergies are hypothesized to reflect connections among motoneurons in the spinal cord activated by central commands and sensory feedback. Robotic rehabilitation of upper limb in post-stroke subjects has shown promising results in terms of improvement of arm function and motor control achieved by reassembling muscle synergies into a set more similar to that of healthy people. However, in stroke survivors the potentially neurophysiological changes induced by robot-mediated learning versus usual care have not yet been investigated. We quantified upper limb motor deficits and the changes induced by rehabilitation in 32 post-stroke subjects through the movement analysis of two virtual untrained tasks of object placing and pronation. The sample analyzed in this study is part of a larger bi-center study and included all subjects who underwent kinematic analysis and were randomized into robot and usual care groups. Post-stroke subjects who followed robotic rehabilitation showed larger improvements in axial-to-proximal muscle synergies with respect to those who underwent usual care. This was associated to a significant improvement of the proximal kinematics. Both treatments had negative effects in muscle synergies controlling the distal district. This study supports the definition of new rehabilitative treatments for improving the neurophysiological recovery after stroke.
In vitro and in vivo inhibition of malaria parasite infection by monoclonal antibodies against Plasmodium falciparum circumsporozoite protein (CSP)
Authors: Livingstone Merricka C. , Bitzer Alexis A. , Giri Alish , Luo Kun , Sankhala Rajeshwer S. , Choe Misook , Zou Xiaoyan , Dennison S. Moses , Li Yuanzhang , Washington William , Ngauy Viseth , Tomaras Georgia D. , Joyce M. Gordon , Batchelor Adrian H. , Dutta Sheetij 
Published: March 2021

AbstractPlasmodium falciparum malaria contributes to a significant global disease burden. Circumsporozoite protein (CSP), the most abundant sporozoite stage antigen, is a prime vaccine candidate. Inhibitory monoclonal antibodies (mAbs) against CSP map to either a short junctional sequence or the central (NPNA)n repeat region. We compared in vitro and in vivo activities of six CSP-specific mAbs derived from human recipients of a recombinant CSP vaccine RTS,S/AS01 (mAbs 317 and 311); an irradiated whole sporozoite vaccine PfSPZ (mAbs CIS43 and MGG4); or individuals exposed to malaria (mAbs 580 and 663). RTS,S mAb 317 that specifically binds the (NPNA)n epitope, had the highest affinity and it elicited the best sterile protection in mice. The most potent inhibitor of sporozoite invasion in vitro was mAb CIS43 which shows dual-specific binding to the junctional sequence and (NPNA)n. In vivo mouse protection was associated with the mAb reactivity to the NANPx6 peptide, the in vitro inhibition of sporozoite invasion activity, and kinetic parameters measured using intact mAbs or their Fab fragments. Buried surface area between mAb and its target epitope was also associated with in vivo protection. Association and disconnects between in vitro and in vivo readouts has important implications for the design and down-selection of the next generation of CSP based interventions.
The association between body mass index and recovery from post-traumatic stress disorder after the nuclear accident in Fukushima
Authors: Nagai Masato , Ohira Tetsuya , Maeda Masaharu , Yasumura Seiji , Miura Itaru , Itagaki Shuntaro , Harigane Mayumi , Takase Kanae , Yabe Hirooki , Sakai Akira , Kamiya Kenji 
Published: March 2021

AbstractPost-traumatic stress disorder (PTSD) and obesity share common risk factors; however, the effect of obesity on recovery from PTSD has not been assessed. We examined the association between body mass index (BMI) and recovery from PTSD after the Great East Japan Earthquake. We analyzed 4356 men and women with probable PTSD aged ≥ 16 years who were living in evacuation zones owing to the radiation accident in Fukushima, Japan. Recovery from probable PTSD was defined as Post-traumatic Stress Disorder Checklist-specific scores < 44. Using Poisson regression with robust error variance adjusted for confounders, we compared the prevalence ratios (PRs) and 95% confidence intervals (CIs) for this outcome in 2013 and 2014. Compared with point estimates for normal weight (BMI: 18.5–24.9 kg/m2), especially in 2013, those for underweight (BMI: < 18.5 kg/m2) and obesity (BMI: ≥ 30.0 kg/m2) tended to slightly increase and decrease, respectively, for recovery from probable PTSD. The multivariate-adjusted PRs (95% CIs) for underweight and obesity were 1.08 (0.88–1.33) and 0.85 (0.68–1.06), respectively, in 2013 and 1.02 (0.82–1.26) and 0.87 (0.69–1.09), respectively, in 2014. The results of the present study showed that obesity may be a useful predictor for probable PTSD recovery. Obese victims with PTSD would require more intensive support and careful follow-up for recovery.
Population imaging discrepancies between a genetically-encoded calcium indicator (GECI) versus a genetically-encoded voltage indicator (GEVI)
Authors: Zhu Mei Hong , Jang Jinyoung , Milosevic Milena M. , Antic Srdjan D. 
Published: March 2021

AbstractGenetically-encoded calcium indicators (GECIs) are essential for studying brain function, while voltage indicators (GEVIs) are slowly permeating neuroscience. Fundamentally, GECI and GEVI measure different things, but both are advertised as reporters of “neuronal activity”. We quantified the similarities and differences between calcium and voltage imaging modalities, in the context of population activity (without single-cell resolution) in brain slices. GECI optical signals showed 8–20 times better SNR than GEVI signals, but GECI signals attenuated more with distance from the stimulation site. We show the exact temporal discrepancy between calcium and voltage imaging modalities, and discuss the misleading aspects of GECI imaging. For example, population voltage signals already repolarized to the baseline (~ disappeared), while the GECI signals were still near maximum. The region-to-region propagation latencies, easily captured by GEVI imaging, are blurred in GECI imaging. Temporal summation of GECI signals is highly exaggerated, causing uniform voltage events produced by neuronal populations to appear with highly variable amplitudes in GECI population traces. Relative signal amplitudes in GECI recordings are thus misleading. In simultaneous recordings from multiple sites, the compound EPSP signals in cortical neuropil (population signals) are less distorted by GEVIs than by GECIs.
Variability in mRNA translation: a random matrix theory approach
Authors: Margaliot Michael , Huleihel Wasim , Tuller Tamir 
Published: March 2021

AbstractThe rate of mRNA translation depends on the initiation, elongation, and termination rates of ribosomes along the mRNA. These rates depend on many “local” factors like the abundance of free ribosomes and tRNA molecules in the vicinity of the mRNA molecule. All these factors are stochastic and their experimental measurements are also noisy. An important question is how protein production in the cell is affected by this considerable variability. We develop a new theoretical framework for addressing this question by modeling the rates as identically and independently distributed random variables and using tools from random matrix theory to analyze the steady-state production rate. The analysis reveals a principle of universality: the average protein production rate depends only on the of the set of possible values that the random variable may attain. This explains how total protein production can be stabilized despite the overwhelming stochasticticity underlying cellular processes.
A robot-aided visuomotor wrist training induces gains in proprioceptive and movement accuracy in the contralateral wrist
Authors: Wang Yizhao , Zhu Huiying , Elangovan Naveen , Cappello Leonardo , Sandini Giulio , Masia Lorenzo , Konczak Jürgen 
Published: March 2021

AbstractProprioceptive training is a neurorehabilitation approach known to improve proprioceptive acuity and motor performance of a joint/limb system. Here, we examined if such learning transfers to the contralateral joints. Using a robotic exoskeleton, 15 healthy, right-handed adults (18–35 years) trained a visuomotor task that required making increasingly small wrist movements challenging proprioceptive function. Wrist position sense just-noticeable-difference thresholds (JND) and spatial movement accuracy error (MAE) in a wrist-pointing task that was not trained were assessed before and immediately as well as 24 h after training. The main results are: first, training reduced JND thresholds (− 27%) and MAE (− 33%) in the trained right wrist. Sensory and motor gains were observable 24 h after training. Second, in the untrained left wrist, mean JND significantly decreased (− 32%) at posttest. However, at retention the effect was no longer significant. Third, motor error at the untrained wrist declined slowly. Gains were not significant at posttest, but MAE was significantly reduced (− 27%) at retention. This study provides first evidence that proprioceptive-focused visuomotor training can induce proprioceptive and motor gains not only in the trained joint but also in the contralateral, homologous joint. We discuss the possible neurophysiological mechanism behind such sensorimotor transfer and its implications for neurorehabilitation.
Associations between dog keeping and indoor dust microbiota
Authors: Mäki Jenni M. , Kirjavainen Pirkka V. , Täubel Martin , Piippo-Savolainen Eija , Backman Katri , Hyvärinen Anne , Tuoresmäki Pauli , Jayaprakash Balamuralikrishna , Heinrich Joachim , Herberth Gunda , Standl Marie , Pekkanen Juha , Karvonen Anne M. 
Published: March 2021

AbstractLiving with dogs appears to protect against allergic diseases and airway infections, an effect possibly linked with immunomodulation by microbial exposures associated with dogs. The aim of this study was to characterize the influence of dog ownership on house dust microbiota composition. The bacterial and fungal microbiota was characterized with Illumina MiSeq sequencing from floor dust samples collected from homes in a Finnish rural-suburban (LUKAS2, N = 182) birth cohort, and the results were replicated in a German urban (LISA, N = 284) birth cohort. Human associated bacteria variable was created by summing up the relative abundances of five bacterial taxa. Bacterial richness, Shannon index and the relative abundances of seven bacterial genera, mostly within the phyla Proteobacteria and Firmicutes, were significantly higher in the dog than in the non-dog homes, whereas the relative abundance of human associated bacteria was lower. The results were largely replicated in LISA. Fungal microbiota richness and abundance of Leucosporidiella genus were higher in dog homes in LUKAS2 and the latter association replicated in LISA. Our study confirms that dog ownership is reproducibly associated with increased bacterial richness and diversity in house dust and identifies specific dog ownership-associated genera. Dogs appeared to have more limited influence on the fungal than bacterial indoor microbiota.