bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel retinal ganglion cell quantification tool based on deep learning
Authors: Masin Luca , Claes Marie , Bergmans Steven , Cools Lien , Andries Lien , Davis Benjamin M. , Moons Lieve , De Groef Lies 
Published: January 2021

AbstractGlaucoma is a disease associated with the loss of retinal ganglion cells (RGCs), and remains one of the primary causes of blindness worldwide. Major research efforts are presently directed towards the understanding of disease pathogenesis and the development of new therapies, with the help of rodent models as an important preclinical research tool. The ultimate goal is reaching neuroprotection of the RGCs, which requires a tool to reliably quantify RGC survival. Hence, we demonstrate a novel deep learning pipeline that enables fully automated RGC quantification in the entire murine retina. This software, called RGCode (Retinal Ganglion Cell quantification based On DEep learning), provides a user-friendly interface that requires the input of RBPMS-immunostained flatmounts and returns the total RGC count, retinal area and density, together with output images showing the computed counts and isodensity maps. The counting model was trained on RBPMS-stained healthy and glaucomatous retinas, obtained from mice subjected to microbead-induced ocular hypertension and optic nerve crush injury paradigms. RGCode demonstrates excellent performance in RGC quantification as compared to manual counts. Furthermore, we convincingly show that RGCode has potential for wider application, by retraining the model with a minimal set of training data to count FluoroGold-traced RGCs.
Outcome of TACE treatment in HIV infected patients with hepatocellular carcinoma
Authors: Kong Lingxiang , Wei Guo , Lv Tao , Jiang Li , Yang Jian , Zhao Yong , Yang Jiayin 
Published: January 2021

AbstractThe surgical treatment and transcatheter arterial chemoembolization (TACE) rate of human immunodeficiency virus (HIV)-infected hepatocellular carcinoma (HCC) patients is relatively low in West China. For various reasons, most patients do not receive timely surgical treatment. Upon transfer to an infectious disease centralized hospital, they were already classified in the Barcelona Clinic Liver Cancer (BCLC)-B stage. A total of 2249 BCLC-B HCC patients were analyzed. The eligible population was divided into three groups for analysis of survival and prognostic factors; These were 21 HIV infected (HIV+) HCC patients treated with TACE (TACE+), 1293 non-HIV-infected (HIV−) HCC patients treated with TACE, and 150 HIV− HCC patients who only receive medication (TACE−) as a second control group. After 1:2 matching, 1- and 2-year survival of HIV+ TACE+ and HIV− TACE+ groups was 64.3% and 76.5% (P = 0.453) and 45.5% vs. 50.0% (P = 0.790) respectively. We also compared one and two-year survival between HIV+ TACE+ and HIV− TACE−. One-year overall survival was 64.3% vs. 45.7% (P = 0.097) and 2-year survival was 45.5% vs. 7.1% (P = 0.004). Multivariate analysis showed that the most important prognostic factors for survival were serum alpha-fetoprotein (AFP) and Child–Pugh score and tumor size, while HIV status had no significant effect on prognosis statistically. CD4 levels below 200 may increase the risk of opportunistic infection after surgery, but after anti-infection and systematic supportive therapy, it has no effect on survival. HIV+ patients should have the same treatment opportunities as HIV− patients. If the patient's immune status permits, we suggest that early TACE treatment should be administered to BCLC-B HCC patients, regardless of HIV infection.
Templating the morphology of soft microgel assemblies using a nanolithographic 3D-printed membrane
Authors: Linkhorst John , Lölsberg Jonas , Thill Sebastian , Lohaus Johannes , Lüken Arne , Naegele Gerhard , Wessling Matthias 
Published: January 2021

AbstractFilter cake formation is the predominant phenomenon limiting the filtration performance of membrane separation processes. However, the filter cake’s behavior at the particle scale, which determines its overall cake behavior, has only recently come into the focus of scientists, leaving open questions about its formation and filtration behavior. The present study contributes to the fundamental understanding of soft filter cakes by analyzing the influence of the porous membrane’s morphology on crystal formation and the compaction behavior of soft filter cakes under filtration conditions. Microfluidic chips with nanolithographic imprinted filter templates were used to trigger the formation of crystalline colloidal filter cakes formed by soft microgels. The soft filter cakes were observed via confocal laser scanning microscopy (CLSM) under dead-end filtration conditions. Colloidal crystal formation in the cake, as well as their compaction behavior, were analyzed by optical visualization and pressure data. For the first time, we show that exposing the soft cake to a crystalline filter template promotes the formation of colloidal crystallites and that soft cakes experience gradient compression during filtration.
Chemical enhanced oil recovery and the dilemma of more and cleaner energy
Authors: Farajzadeh Rouhi , Kahrobaei Siavash , Eftekhari Ali Akbari , Mjeni Rifaat A. , Boersma Diederik , Bruining Johannes 
Published: January 2021

AbstractA method based on the concept of exergy-return on exergy-investment is developed to determine the energy efficiency and CO2 intensity of polymer and surfactant enhanced oil recovery techniques. Exergy is the useful work obtained from a system at a given thermodynamics state. The main exergy investment in oil recovery by water injection is related to the circulation of water required to produce oil. At water cuts (water fraction in the total liquid produced) greater than 90%, more than 70% of the total invested energy is spent on injection and lift pumps, resulting in large CO2 intensity for the produced oil. It is shown that injection of polymer with or without surfactant can considerably reduce CO2 intensity of the mature waterflood projects by decreasing the volume of produced water and the exergy investment associated with its circulation. In the field examples considered in this paper, a barrel of oil produced by injection of polymer has 2–5 times less CO2 intensity compared to the baseline waterflood oil. Due to large manufacturing exergy of the synthetic polymers and surfactants, in some cases, the unit exergy investment for production of oil could be larger than that of the waterflooding. It is asserted that polymer injection into reservoirs with large water cut can be a solution for two major challenges of the energy transition period: (1) meet the global energy demand via an increase in oil recovery and (2) reduce the CO2 intensity of oil production (more and cleaner energy).
Alterations observed in the interferon α and β signaling pathway in MDD patients are marginally influenced by cis-acting alleles
Authors: Magri Chiara , Giacopuzzi Edoardo , Sacco Chiara , Bocchio-Chiavetto Luisella , Minelli Alessandra , Gennarelli Massimo 
Published: January 2021

AbstractMajor depressive disorder (MDD) is a common psychiatric disorder with a multifactorial aetiology determined by the interaction between genetic and environmental risk factors. Pieces of evidence indicate that inflammation and immune activation may contribute to the onset of MDD playing a role in the pathogenetic mechanism. To date, it is not known to which extent the association between MDD and inflammation is shaped by the genetic background or by the presence of environmental factors. To clarify this issue, we analyzed genotype and blood RNA profiles of 463 MDD cases and 459 controls (NIMH-Study 88/Site621) estimating the Genetic and Environmental Regulated eXpression component of gene expression (GReX and EReX respectively). Both components were tested for association with MDD. Many genes belonging to the α/β interferon signaling pathway showed an association between MDD and EReX, only two between MDD and GReX. Also other MDD differentially expressed genes were more influenced by the EReX than by GReX. These results suggest that impact of the genetic background on MDD blood gene expression alterations is much lower than the contribution of environmental factors and almost absent for the genes of the interferon pathway.
Sterol auto-oxidation adversely affects human motor neuron viability and is a neuropathological feature of amyotrophic lateral sclerosis
Authors: Dodge James C. , Yu Jinlong , Sardi S. Pablo , Shihabuddin Lamya S. 
Published: January 2021

AbstractAberrant cholesterol homeostasis is implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS), a fatal neuromuscular disease that is due to motor neuron (MN) death. Cellular toxicity from excess cholesterol is averted when it is enzymatically oxidized to oxysterols and bile acids (BAs) to promote its removal. In contrast, the auto oxidation of excess cholesterol is often detrimental to cellular survival. Although oxidized metabolites of cholesterol are altered in the blood and CSF of ALS patients, it is unknown if increased cholesterol oxidation occurs in the SC during ALS, and if exposure to oxidized cholesterol metabolites affects human MN viability. Here, we show that in the SOD1G93A mouse model of ALS that several oxysterols, BAs and auto oxidized sterols are increased in the lumbar SC, plasma, and feces during disease. Similar changes in cholesterol oxidation were found in the cervical SC of sporadic ALS patients. Notably, auto-oxidized sterols, but not oxysterols and BAs, were toxic to iPSC derived human MNs. Thus, increased cholesterol oxidation is a manifestation of ALS and non-regulated sterol oxidation likely contributes to MN death. Developing therapeutic approaches to restore cholesterol homeostasis in the SC may lead to a treatment for ALS.
Association of nocebo hyperalgesia and basic somatosensory characteristics in a large cohort
Authors: Feldhaus Mari Hanna , Horing Björn , Sprenger Christian , Büchel Christian 
Published: January 2021

AbstractMedical outcomes are strongly affected by placebo and nocebo effects. Prediction of who responds to such expectation effects has proven to be challenging. Most recent approaches to prediction have focused on placebo effects in the context of previous treatment experiences and expectancies, or personality traits. However, a recent model has suggested that basic somatosensory characteristics play an important role in expectation responses. Consequently, this study investigated not only the role of psychological variables, but also of basic somatosensory characteristics. In this study, 624 participants underwent a placebo and nocebo heat pain paradigm. Additionally, individual psychological and somatosensory characteristics were assessed. While no associations were identified for placebo responses, nocebo responses were associated with personality traits (e.g. neuroticism) and somatosensory characteristics (e.g. thermal pain threshold). Importantly, the associations between somatosensory characteristics and nocebo responses were among the strongest. This study shows that apart from personality traits, basic somatosensory characteristics play an important role in individual nocebo responses, in agreement with the novel idea that nocebo responses result from the integration of top-down expectation and bottom-up sensory information.
Spatiotemporal dynamic characteristics of typical temperate glaciers in China
Authors: Shijin Wang , Yanjun Che , Yanqiang Wei 
Published: January 2021

AbstractChina’s temperate glaciers have a relatively warm and humid climate and hydrothermal conditions at low latitudes. Temperate glaciers, however, have larger ablation, higher ice temperatures, relatively fast movement speeds, and a significant sliding process at the bottom. As a result, these glaciers are more significantly affected by climate change. On the basis of topographic maps, aerial photography, and Landsat OLI images, and combined with existing research results, this paper systematically analyzed the temporal and spatial dynamic characteristics of typical temperate glaciers. The results are as follows: (1) From the 1950s to the 1970s, compared with other types of glaciers, temperate glaciers showed strong retreat and ablation trends in terms of area, length, speed, and mass balance. (2) The reduction rates of glacier areas of Kangri Garpo, Dagu Snow Mountain, Yulong Snow Mountain (YSM), and Meili Snow Mountain (MSM) in China’s temperate glacier areas all exceeded 38%, which was far above the national average of 18% from the 1950s to the 2010s. (3) The recent length retreat rates of Azha Glacier, Kangri Garpo, and Mingyong Glacier, MSM, Hailuogou Glacier (HG), Gongga Snow Mountain (GSM), and Baishui River Glacier No. 1 (BRGN1), YSM were above 22 m/a, which was faster than the retreat rates of other regions. (4) Consistent with glacier retreat, temperate glaciers also had a faster ice flow speed. The ice flow velocities of the BGN1, HG, Parlung River Glaciers No. 4 and 94, and Nyainqêntanglha were, respectively, 6.33–30.78 m/a, 41–205 m/a, 15.1–86.3 m/a, and 7.5–18.4 m/a, which was much faster than the velocity of other types of glaciers. (5) Mass loss of temperate glaciers was most dramatic during the observation period (1959–2015). The annual mass balance from eight typical temperate glaciers fluctuated between − 2.48 and 0.44 m w.e., and the annual average change rate of mass balance (− 0.037 m w.e./a) was much higher than that in China (− 0.015 m w.e./a, p < 0.0001) and globally (− 0.013 m w.e./a, p < 0.0001).
Near-term climate change impacts on sub-national malaria transmission
Authors: Lubinda Jailos , Haque Ubydul , Bi Yaxin , Hamainza Busiku , Moore Adrian J. 
Published: January 2021

AbstractThe role of climate change on global malaria is often highlighted in World Health Organisation reports. We modelled a Zambian socio-environmental dataset from 2000 to 2016, against malaria trends and investigated the relationship of near-term environmental change with malaria incidence using Bayesian spatio-temporal, and negative binomial mixed regression models. We introduced the diurnal temperature range (DTR) as an alternative environmental measure to the widely used mean temperature. We found substantial sub-national near-term variations and significant associations with malaria incidence-trends. Significant spatio-temporal shifts in DTR/environmental predictors influenced malaria incidence-rates, even in areas with declining trends. We highlight the impact of seasonally sensitive DTR, especially in the first two quarters of the year and demonstrate how substantial investment in intervention programmes is negatively impacted by near-term climate change, most notably since 2010. We argue for targeted seasonally-sensitive malaria chemoprevention programmes.
Probiotic lactobacilli as a promising strategy to ameliorate disorders associated with intestinal inflammation induced by a non-steroidal anti-inflammatory drug
Authors: Monteros María José Martínez , Galdeano Carolina Maldonado , Balcells María Florencia , Weill Ricardo , De Paula Juan Andrés , Perdigón Gabriela , Cazorla Silvia Inés 
Published: January 2021

AbstractDamage to the small intestine caused by non-steroidal anti-inflammatory drugs (NSAIDs) occurs more frequently than in the upper gastrointestinal tract, is more difficult to diagnose and no effective treatments exist. Hence, we investigated whether probiotics can control the onset of this severe condition in a murine model of intestinal inflammation induced by the NSAID, indomethacin. Probiotic supplementation to mice reduce the body weight loss, anemia, shortening of the small intestine, cell infiltration into the intestinal tissue and the loss of Paneth and Goblet cells associated with intestinal inflammation. Furthermore, a high antimicrobial activity in the intestinal fluids of mice fed with probiotics compared to animals on a conventional diet was elicited against several pathogens. Interestingly, probiotics dampened the oxidative stress and several local and systemic markers of an inflammatory process, as well as increased the secretion of IL-10 by regulatory T cells. Even more importantly, probiotics induced important changes in the large intestine microbiota characterized by an increase in anaerobes and lactobacilli, and a significant decrease in total enterobacteria. We conclude that oral probiotic supplementation in NSAID-induced inflammation increases intestinal antimicrobial activity and reinforces the intestinal epithelial barrier in order to avoid pathogens and commensal invasion and maintain intestinal homeostasis.
Wisdom of crowds benefits perceptual decision making across difficulty levels
Authors: Saha Roy Tiasha , Mazumder Satyaki , Das Koel 
Published: January 2021

AbstractDecades of research on collective decision making has claimed that aggregated judgment of multiple individuals is more accurate than expert individual judgement. A longstanding problem in this regard has been to determine how decisions of individuals can be combined to form intelligent group decisions. Our study consisted of a random target detection task in natural scenes, where human subjects (18 subjects, 7 female) detected the presence or absence of a random target as indicated by the cue word displayed prior to stimulus display. Concurrently the neural activities (EEG signals) were recorded. A separate behavioural experiment was performed by different subjects (20 subjects, 11 female) on the same set of images to categorize the tasks according to their difficulty levels. We demonstrate that the weighted average of individual decision confidence/neural decision variables produces significantly better performance than the frequently used majority pooling algorithm. Further, the classification error rates from individual judgement were found to increase with increasing task difficulty. This error could be significantly reduced upon combining the individual decisions using group aggregation rules. Using statistical tests, we show that combining all available participants is unnecessary to achieve minimum classification error rate. We also try to explore if group aggregation benefits depend on the correlation between the individual judgements of the group and our results seem to suggest that reduced inter-subject correlation can improve collective decision making for a fixed difficulty level.
CYP3A4 mediated pharmacokinetics drug interaction potential of Maha-Yogaraj Gugglu and E, Z guggulsterone
Authors: Sabarathinam Sarvesh , Rajappan Chandra Satish Kumar , Thangavel Mahalingam Vijayakumar 
Published: January 2021

AbstractMaha yogaraja guggulu (MYG) is a classical herbomineral polyherbal formulation being widely used since centuries. The aim of this study was to investigate the effect of MYG formulation and its major constituents E & Z guggulsterone on CYP3A4 mediated metabolism. In vitro inhibition of MYG and Guggulsterone isomers on CYP3A4 was evaluated by high throughput fluorometric assay. Eighteen Adult male Sprague–Dawley rats (200 ± 25 g body weight) were randomly divided into three groups. Group A, Group B and Group C were treated with placebo, MYG and Standard E & Z guggulsterone for 14 days respectively by oral route. On 15th day, midazolam (5 mg/kg) was administered orally to all rats in each group. Blood samples (0.3 mL) were collected from the retro orbital vein at 0.25, 0.5, 0.75, 1, 2, 4, 6, 12 and 24 h of each rat were collected. The findings from the in vitro & in vivo study proposed that the MYG tablets and its guggulsterone isomers have drug interaction potential when consumed along with conventional drugs which are CYP3A4 substrates. In vivo pharmacokinetic drug interaction study of midazolam pointed out that the MYG tablets and guggulsterone isomers showed an inhibitory activity towards CYP3A4 which may have leads to clinically significant interactions.
Novel approach to enhance coastal habitat and biotope mapping with drone aerial imagery analysis
Authors: Monteiro João Gama , Jiménez Jesús L. , Gizzi Francesca , Přikryl Petr , Lefcheck Jonathan S. , Santos Ricardo S. , Canning-Clode João 
Published: January 2021

AbstractUnderstanding the complex factors and mechanisms driving the functioning of coastal ecosystems is vital towards assessing how organisms, ecosystems, and ultimately human populations will cope with the ecological consequences of natural and anthropogenic impacts. Towards this goal, coastal monitoring programs and studies must deliver information on a range of variables and factors, from taxonomic/functional diversity and spatial distribution of habitats, to anthropogenic stress indicators such as land use, fisheries use, and pollution. Effective monitoring programs must therefore integrate observations from different sources and spatial scales to provide a comprehensive view to managers. Here we explore integrating aerial surveys from a low-cost Remotely Piloted Aircraft System (RPAS) with concurrent underwater surveys to deliver a novel approach to coastal monitoring. We: (i) map depth and substrate of shallow rocky habitats, and; (ii) classify the major biotopes associated with these environmental axes; and (iii) combine data from i and ii to assess the likely distribution of common sessile organismal assemblages over the survey area. Finally, we propose a general workflow that can be adapted to different needs and aerial platforms, which can be used as blueprints for further integration of remote-sensing with in situ surveys to produce spatially-explicit biotope maps.
Targeted sequencing to identify genetic alterations and prognostic markers in pediatric T-cell acute lymphoblastic leukemia
Authors: Chang Ya-Hsuan , Yu Chih-Hsiang , Jou Shiann-Tarng , Lin Chien-Yu , Lin Kai-Hsin , Lu Meng-Yao , Wu Kang-Hsi , Chang Hsiu-Hao , Lin Dong-Tsamn , Lin Shu-Wha , Chen Hsuan-Yu , Yang Yung-Li 
Published: January 2021

AbstractT-cell acute lymphoblastic leukemia (T-ALL) is caused by the accumulation of multiple genetic alterations. To determine the frequency of common genetic mutations and possible prognostic markers in childhood T-ALL, we performed targeted sequencing of 67 genes across 64 cases treated according to Taiwan Pediatric Oncology Group protocols between January 2002 and December 2015. Together, 302 variants were identified in 60 genes including 233 single nucleotide variants and 69 indels. Sixty-four samples had a median number of six genetic lesions each (range 1–17). Thirteen genes had mutation frequencies > 10%, and 5 were > 20%, with the highest being NOTCH1 (70.31%). Protocadherins FAT1 (32.81%) and FAT3 (17.19%), and the ubiquitin ligase component FBXW7 (28.13%) had higher mutation frequencies than previously reported. Other mutation frequencies (PHF6, DNM2, DNMT3A, CNOT3, and WT1) were within previously reported ranges. Three epigenetic-related genes (KMT2D, DNMT3A, and EZH2) were mutated in our cohort. JAK-STAT signaling pathway genes had mutation frequencies of 3–13% and were observed in 23 cases (35.94%). Changes to genes in the ErbB signaling pathway were detected in 20 cases (31.25%). Patients with NOTCH1/FBXW7 mutations and RAS/PTEN germline exhibited better 5-year overall survival rates.