bluuebunny/crossref_metadata_2025 huggingface dataset:
Impacts of streamflow alteration on benthic macroinvertebrates by mini-hydro diversion in Sri Lanka
Authors: Munasinghe Dinuke S. N. , Najim Mohamed M. M. , Quadroni Silvia , Musthafa Muneeb M.
Published: January 2021

Our study focused on quantifying the alterations of streamflow at a weir site due to the construction of a mini-hydropower plant in the Gurugoda Oya (Sri Lanka), and evaluating the spatial responses of benthic macroinvertebrates to altered flow regime. The HEC–HMS 3.5 model was applied to the Gurugoda Oya sub-catchment to generate streamflows for the time period 1991–2013. Pre-weir flows were compared to post-weir flows with 32 Indicators of Hydrologic Alteration using the range of variability approach (RVA). Concurrently, six study sites were established upstream and downstream of the weir, and benthic macroinvertebrates were sampled monthly from May to November 2013 (during the wet season). The key water physico-chemical parameters were also determined. RVA analysis showed that environmental flow was not maintained below the weir. The mean rate of non-attainment was ~ 45% suggesting a moderate level of hydrologic alteration. Benthic macroinvertebrate communities significantly differed between the study sites located above and below the weir, with a richness reduction due to water diversion. The spatial distribution of zoobenthic fauna was governed by water depth, dissolved oxygen content and volume flow rate. Our work provides first evidence on the effects of small hydropower on river ecosystem in a largely understudied region. Studies like this are important to setting-up adequate e-flows.
High molecular pyrogens present in plant extracts interfere with examinations of their immunomodulatory properties in vitro
Authors: Kruk Aleksandra , Piwowarski Jakub P. , Pawłowska Karolina A. , Popowski Dominik , Granica Sebastian
Published: January 2021

The widely accepted strategy to justify the use of medicinal plant extracts in diseases with inflammatory background is their examination on in vitro models using immune cells. It is also a key initial step of research for active principles, which could be then isolated and tested on more advanced models, becoming new pharmacologically active lead molecules. The crucial aspect which has not been so far addressed in this context, is the presence of pyrogens in plant preparations. The aim of this study was the examination of pyrogens interference with in vitro evaluation of anti-inflammatory activity of plant extracts using human primary neutrophils model together with introduction of effective method of interfering factors elimination. The obtained results showed that chosen plant extracts contained pyrogens, which were responsible for concentration-dependent stimulation of pro-inflammatory cytokines production by human neutrophils in vitro in the same extent as LPS did. The ultrafiltration method was successfully applied for pyrogens elimination, which effectiveness was confirmed using LAL test. The determined interference of pyrogens implies the necessity of their consideration and removal when in vitro studies include direct addition of plant extracts to the cell culture, what can be obtained by ultrafiltration, which does not affect extract composition.
Elucidation of high permeability water among VACNFs using molecular dynamics
Authors: Matsuzaki Ryosuke , Chisaka Yusuke , Tajiri Tomohiro
Published: January 2021

The cause of the high permeability in the flow of water in CNT (carbon nanotube)-based nanoscale materials remains to be elucidated. In this study, water impregnation simulations outside the VACNFs were performed using the molecular dynamics method to investigate the factors that cause high permeability by virtually changing the force field parameters. As a result, the permeability coefficient increased with increasing CNT content (VC) in the slip flow region. For the constant VC, the smaller the intermolecular force between water and CNTs, the higher the permeability coefficient. Because the intermolecular forces between water and CNTs are smaller than those between water and water, it may have an effect on the high permeability phenomenon. Furthermore, in the present VC change, the arrangement structure of the water molecules changed from a disordered structure, such as bulk flow, to a chain structure in the impregnation direction, which is also considered a factor for the increase in the permeability. Therefore, both the intermolecular forces between water and CNTs and structural change in the arrangement of water molecules were factors in the high permeability phenomenon.
Studying local Berry curvature in 2H-WSe2 by circular dichroism photoemission utilizing crystal mirror plane
Authors: Cho Soohyun , Park Jin-Hong , Huh Soonsang , Hong Jisook , Kyung Wonshik , Park Byeong-Gyu , Denlinger J. D. , Shim Ji Hoon , Kim Changyoung , Park Seung Ryong
Published: January 2021

It was recently reported that circular dichroism in angle-resolved photoemission spectroscopy (CD-ARPES) can be used to observe the Berry curvature in 2H-WSe2 (Cho et al. in Phys Rev Lett 121:186401, 2018). In that study, the mirror plane of the experiment was intentionally set to be perpendicular to the crystal mirror plane, such that the Berry curvature becomes a symmetric function about the experimental mirror plane. In the present study, we performed CD-ARPES on 2H-WSe2 with the crystal mirror plane taken as the experimental mirror plane. Within such an experimental constraint, two experimental geometries are possible for CD-ARPES. The Berry curvature distributions for the two geometries are expected to be antisymmetric about the experimental mirror plane and exactly opposite to each other. Our experimental CD intensities taken with the two geometries were found to be almost opposite near the corners of the 2D projected hexagonal Brillouin zone (BZ) and were almost identical near the center of the BZ. This observation is well explained by taking the Berry curvature or the atomic orbital angular momentum (OAM) into account. The Berry curvature (or OAM) contribution to the CD intensities can be successfully extracted through a comparison of the CD-ARPES data for the two experimental geometries. Thus, the CD-ARPES experimental procedure described provides a method for mapping Berry curvature in the momentum space of topological materials, such as Weyl semimetals.
Sequential transfer learning based on hierarchical clustering for improved performance in deep learning based food segmentation
Authors: Siemon Mia S. N. , Shihavuddin A. S. M. , Ravn-Haren Gitte
Published: January 2021

Accurately segmenting foods from optical images is a challenging task, yet becoming possible with the help of recent advances in Deep Learning based solutions. Automated identification of food items opens up possibilities of useful applications like nutrition intake monitoring. Given large variations in food choices, Deep Learning based solutions still struggle to generate human level accuracy. In this work, we propose a novel Sequential Transfer Learning method using Hierarchical Clustering. This novel approach simulates a step by step problem solving framework based on clustering of similar types of foods. The proposed approach provides up to 6% gain in accuracy compared to traditional network training and generated a robust model performing better in challenging unseen cases. This approach is also tested for segmenting foods in Danish school children meals for dietary intake monitoring as an application.
Hair follicle germs containing vascular endothelial cells for hair regenerative medicine
Authors: Kageyama Tatsuto , Chun Yang-Sook , Fukuda Junji
Published: January 2021

Hair regenerative medicine has emerged as a promising approach for the treatment of severe hair loss. Recent advances in three-dimensional tissue engineering, such as formation of hair follicle germs (HFGs), have considerably improved hair regeneration after transplantation in animal models. Here, we proposed an approach for fabricating HFGs containing vascular endothelial cells. Epithelial, dermal papilla, and vascular endothelial cells initially formed a single aggregate, which subsequently became a dumbbell-shaped HFG, wherein the vascular endothelial cells localized in the region of dermal papilla cells. The HFGs containing vascular endothelial cells exhibited higher expression of hair morphogenesis-related genes in vitro, along with higher levels of hair shaft regeneration upon transplantation to the dorsal side of nude mice, than those without vascular endothelial cells. The generated hair follicles represented functional characteristics, such as piloerection, as well as morphological characteristics comparable to those of natural hair shafts. This approach may provide a promising strategy for fabricating tissue grafts with higher hair inductivity for hair regenerative medicine.
Bacteriological and mechanical impact of the Sterrad sterilization method on personalized 3D printed guides for mandibular reconstruction
Authors: Bosc Romain , Tortolano Lionel , Hersant Barbara , Oudjhani Moussa , Leplay Céline , Woerther Paul L. , Aguilar Paola , Leguen Ronan , Meningaud Jean-Paul
Published: January 2021

Surgical cutting guides are increasingly used for maxillofacial reconstruction. They are usually provided by laboratories. In recent years, surgical teams have published studies on the possibility of manufacturing their own cutting guides thanks to 3D printers. The object of this study is to analyze the impact of the sterilization on the surface of those personalized models and to assess the effectiveness of sterilization. Using the data from high-resolution CT scan of patient, 3D models were generated through computerized assisted design and fabricated with a 3D printer using Acrylonitrile Butadiene Styrene (ABS). For the sterilization, a Sterrad method was used. In order to evaluate the effectiveness of sterilization, 3D models were artificially contaminated with several bacterial reference strains, sterilized and finally cultured. The surfaces and mechanical modifications were analyzed before and after sterilization with infrared spectrometry, surface contact angle, extensometer, scanning electron microscopy and atomic force microscopy. Ten models of different shapes and 24 samples were fabricated, sterilized and analyzed. The 3D models were designed in 48 h, printed in an average of 122 min and underwent a 47 min cycle of sterilization. All experimentally contaminated 3D models were negative in culture, with at least, a six log reduction of the initial inoculum. The hydrophobicity and roughness of the surface suffered few changes. The reproducibility of this procedure was proved by identical results in the three sterilization rounds. Using Sterrad process for the sterilization of ABS printed material doesn’t represent a bacterial risk for the patient. It is a feasible and safe innovative reconstructive method that can save time particularly for oncological cases.
Absolute configuration by vibrational circular dichroism of anti-inflammatory macrolide briarane diterpenoids from the Gorgonian Briareum asbestinum
Authors: Pech-Puch Dawrin , Joseph-Nathan Pedro , Burgueño-Tapia Eleuterio , González-Salas Carlos , Martínez-Matamoros Diana , Pereira David M. , Pereira Renato B. , Jiménez Carlos , Rodríguez Jaime
Published: January 2021

The four new briarane diterpenoids 2-butyryloxybriarane B-3 (2), 9-acetylbriarenolide S (3), briarenolide W (4), and 12-isobriarenolide P (5), along with briarane B-3 (1) and the five known diterpenes 6–10 were isolated from the gorgonian coral Briareum asbestinum collected from the Mexican Caribbean Sea. The structures were elucidated by 1D and 2D NMR and MS measurements. Since the structure of briarane B-3 (1) was only suggested and published without any spectroscopic support, it was herein confirmed, and the supporting data are now provided. In addition, 1 provided the opportunity to explore the sensitivity of vibrational circular dichroism (VCD) to determine the configuration of a single stereogenic center in the presence of eight other stereogenic centers in a molecule possessing a highly flexible ten-member ring. A single-crystal X-ray diffraction study, in which the Flack and Hooft parameters of 1 were determined, further confirmed that briarane B-3 is (1S,2S,6S,7R,8R,9S,10S,11R,17R)-1. This paper reports for first time the use of VCD in briarane diterpenes and with the presence of chlorine atoms. Biological evaluation of seven isolated compounds evidenced a moderate anti-inflammatory activity for compounds 6 and 9 but it did not show any cytotoxic, antiviral, antibacterial, and topoisomerase inhibitory activity.
Amorphous metal oxide semiconductor thin film, analog memristor, and autonomous local learning for neuromorphic systems
Authors: Kimura Mutsumi , Sumida Ryo , Kurasaki Ayata , Imai Takahito , Takishita Yuta , Nakashima Yasuhiko
Published: January 2021

Artificial intelligence is a promising concept in modern and future societies. Presently, software programs are used but with a bulky computer size and large power consumption. Conversely, hardware systems named neuromorphic systems are suggested, with a compact computer size and low power consumption. An important factor is the number of processing elements that can be integrated. In the present study, three decisive technologies are proposed: (1) amorphous metal oxide semiconductor thin films, one of which, Ga–Sn–O (GTO) thin film, is used. GTO thin film does not contain rare metals and can be deposited by a simple process at room temperature. Here, oxygen-poor and oxygen-rich layers are stacked. GTO memristors are formed at cross points in a crossbar array; (2) analog memristor, in which, continuous and infinite information can be memorized in a single device. Here, the electrical conductance gradually changes when a voltage is applied to the GTO memristor. This is the effect of the drift and diffusion of the oxygen vacancies (Vo); and (3) autonomous local learning, i.e., extra control circuits are not required since a single device autonomously modifies its own electrical characteristic. Finally, a neuromorphic system is assembled using the abovementioned three technologies. The function of the letter recognition is confirmed, which can be regarded as an associative memory, a typical artificial intelligence application.
Precise enhancement quantification in post-operative MRI as an indicator of residual tumor impact is associated with survival in patients with glioblastoma
Authors: Garcia-Ruiz Alonso , Naval-Baudin Pablo , Ligero Marta , Pons-Escoda Albert , Bruna Jordi , Plans Gerard , Calvo Nahum , Cos Monica , Majós Carles , Perez-Lopez Raquel
Published: January 2021

Glioblastoma is the most common primary brain tumor. Standard therapy consists of maximum safe resection combined with adjuvant radiochemotherapy followed by chemotherapy with temozolomide, however prognosis is extremely poor. Assessment of the residual tumor after surgery and patient stratification into prognostic groups (i.e., by tumor volume) is currently hindered by the subjective evaluation of residual enhancement in medical images (magnetic resonance imaging [MRI]). Furthermore, objective evidence defining the optimal time to acquire the images is lacking. We analyzed 144 patients with glioblastoma, objectively quantified the enhancing residual tumor through computational image analysis and assessed the correlation with survival. Pathological enhancement thickness on post-surgical MRI correlated with survival (hazard ratio: 1.98, p < 0.001). The prognostic value of several imaging and clinical variables was analyzed individually and combined (radiomics AUC 0.71, p = 0.07; combined AUC 0.72, p < 0.001). Residual enhancement thickness and radiomics complemented clinical data for prognosis stratification in patients with glioblastoma. Significant results were only obtained for scans performed between 24 and 72 h after surgery, raising the possibility of confounding non-tumor enhancement in very early post-surgery MRI. Regarding the extent of resection, and in agreement with recent studies, the association between the measured tumor remnant and survival supports maximal safe resection whenever possible.
Local knowledge as a tool for prospecting wild food plants: experiences in northeastern Brazil
Authors: de Medeiros Patrícia Muniz , dos Santos Gabriela Maria Cota , Barbosa Déborah Monteiro , Gomes Laílson César Andrade , Santos Élida Monique da Costa , da Silva Rafael Ricardo Vasconcelos
Published: January 2021

This study aims to provide a simple framework to identify wild food plants with potential for popularization based on local knowledge and perception. To this end, we also characterized the distribution of this knowledge in the socio-ecological system. We developed the study in the rural settlement Dom Hélder Câmara in northeastern Brazil. The species with the greatest potential for popularization considering the attributes accessed from local knowledge and perception were Psidium guineense Sw., Genipa americana L., Xanthosoma sagittifolium (L.) Schott and Dioscorea trifida L.f. However, the high variation in local knowledge on wild food plants suggests that species that are not frequently cited can also be promising. The absence of age or gender-related knowledge patterns indicates that studies for prospecting wild food plants in similar socioecological contexts need to reach the population as a whole, rather than focusing on a specific group.
Novel method for evaluating the indication for endoscopic papillectomy in patients with ampullary adenocarcinoma
Authors: Yamamoto Kenjiro , Itoi Takao , Nagata Naoyoshi , Sofuni Atsushi , Tsuchiya Takayoshi , Ishii Kentaro , Tanaka Reina , Tonozuka Ryosuke , Honjo Mitsuyoshi , Mukai Shuntaro , Asai Yasutsugu , Matsunami Yukitoshi , Yamaguchi Hiroshi , Matsubayashi Jun , Joyama Eri , Nagakawa Yuichi
Published: January 2021

This study aimed to determine the clinicopathological features of the subtypes of ampullary carcinoma (AC) to explore the indications for endoscopic papillectomy (EP) in early AC. Fifty-seven patients with AC who underwent curative resection were retrospectively reviewed. The 0/IA stages were significantly more common in the intestinal type (I-type) than in the mixed and pancreatobiliary type (M&PB-type) (90.7% vs 35.7%, P < 0.001). Tis/T1a tumors limited to the ampulla [Tis/T1a(ampulla)] were significantly more likely to be I-type than M&PB-type (74.4% vs 14.3%, P = 0.002). The tub1 rate was significantly higher in the I-type than in the M&PB-type (81.4% vs 35.7%, P = 0.001). In the I-type, the tub1 rate was significantly higher for Tis/T1a(ampulla) than for T1a tumors limited to the sphincter of Oddi (100% vs 42.9%, P = 0.004). These observations suggest that I-type AC with tub1 is an indication for EP. The concordance rate of pathological subtypes between endoscopic biopsy and resected specimens was high (κ = 0.8053, P < 0.001). Tis/T1a(ampulla) showed no lymphovascular or perineural invasion. An endoscopic imaging finding of early AC with I-type and tub1 on biopsy could be an indication for EP. Identifying the pathological subtype of AC by endoscopic biopsy could be a novel preoperative approach for evaluating the indications for EP.
Deep learning-based pupil model predicts time and spectral dependent light responses
Authors: Zandi Babak , Khanh Tran Quoc
Published: January 2021

Although research has made significant findings in the neurophysiological process behind the pupillary light reflex, the temporal prediction of the pupil diameter triggered by polychromatic or chromatic stimulus spectra is still not possible. State of the art pupil models rested in estimating a static diameter at the equilibrium-state for spectra along the Planckian locus. Neither the temporal receptor-weighting nor the spectral-dependent adaptation behaviour of the afferent pupil control path is mapped in such functions. Here we propose a deep learning-driven concept of a pupil model, which reconstructs the pupil’s time course either from photometric and colourimetric or receptor-based stimulus quantities. By merging feed-forward neural networks with a biomechanical differential equation, we predict the temporal pupil light response with a mean absolute error below 0.1 mm from polychromatic (2007 $$\pm$$
±
1 K, 4983 $$\pm$$
±
3 K, 10,138 $$\pm$$
±
22 K) and chromatic spectra (450 nm, 530 nm, 610 nm, 660 nm) at 100.01 ± 0.25 cd/m2. This non-parametric and self-learning concept could open the door to a generalized description of the pupil behaviour.
Mortality trends in an ambulatory multidisciplinary heart failure unit from 2001 to 2018
Authors: Spitaleri Giosafat , Lupón Josep , Domingo Mar , Santiago-Vacas Evelyn , Codina Pau , Zamora Elisabet , Cediel Germán , Santesmases Javier , Diez-Quevedo Crisanto , Troya Maria Isabel , Boldo Maria , Altmir Salvador , Alonso Nuria , González Beatriz , Núñez Julio , Bayes-Genis Antoni
Published: January 2021

To assess mortality trends at 1 and 3 years from 2001 to 2018 in a real-life cohort of HF outpatients from different etiologies with depressed and preserved LVEF. A total of 2368 consecutive patients with HF (mean age 66.4 ± 12.9 years, 71% men, 15.4% with preserved LVEF) admitted to a HF clinic from August 2001 to September 2018 were included in the study. Patients were divided into five quintiles (Q) according to the period of admission. Trends for all-cause and cardiovascular mortality from Q1 to Q5 were assessed by linear regression. Patients with LVEF < 50% had a progressive decrease in the rates of all-cause and cardiovascular death at 1 year (12.1% in Q1 to 6.5% in Q5, p = 0.003; and 8.4% in Q1 to 3.8% in Q5, p = 0.007, respectively) and 3 years (30.5% in Q1 to 17.0% in Q5, p = 0.003; and 23.9% in Q1 to 9.8% in Q5, p = 0.003, respectively). These trends remained significant after adjusting for clinical characteristics and risk. No significant trend in mortality was observed in patients with LVEF ≥ 50%. In a cohort of real-life ambulatory patients with HF, mortality progressively declined in patients with LVEF < 50%, but the same trend was not observed in patients with preserved LVEF.
The diagnostic value of human epididymis protein 4 for endometrial cancer is moderate
Authors: Liu Jing , Han Lili , Jiao Zhen
Published: January 2021

Human epididymis protein 4 (HE4) has been used as a biomarker of endometrial cancer (EC) in clinical practice. However, there remains a lack of systemic research on the critical values of HE4 for diagnosing different clinical stages and pathological types of EC. This study investigated the accuracy of human epididymis protein 4 (HE4) in the diagnosis of EC. Patients who were hospitalized for a chief complaint of abnormal vaginal hemorrhage at Xinjiang Uyghur Autonomous Region People's Hospital between 2014 and 2019 were consecutively included. Pathological biopsy confirmed the diagnosis of EC; there were a total of 136 EC patients and 127 non-EC patients. The accuracy of HE4 in the diagnosis of EC was assessed with SPSS software. The accuracy of HE4 for diagnosing different clinical stages and pathological types of EC was also explored. The critical value of HE4 for endometrial cancer was 52.40 mmol/L, with a sensitivity of 57.35% and a specificity of 76.38%. For different stages of EC, the critical value was 36.9 mmol/L, and the sensitivity and specificity were 28% and 87.39%, respectively. For different pathological types, the critical value was 30.60 mmol/L, and the sensitivity and specificity were 93.85% and 33.33%, respectively. The diagnostic value of HE4 for EC is moderate, and the serum HE4 level cannot reflect the stage and type of EC.
Automated detection of mouse scratching behaviour using convolutional recurrent neural network
Authors: Kobayashi Koji , Matsushita Seiji , Shimizu Naoyuki , Masuko Sakura , Yamamoto Masahito , Murata Takahisa
Published: January 2021

Scratching is one of the most important behaviours in experimental animals because it can reflect itching and/or psychological stress. Here, we aimed to establish a novel method to detect scratching using deep neural network. Scratching was elicited by injecting a chemical pruritogen lysophosphatidic acid to the back of a mouse, and behaviour was recorded using a standard handy camera. Images showing differences between two consecutive frames in each video were generated, and each frame was manually labelled as showing scratching behaviour or not. Next, a convolutional recurrent neural network (CRNN), composed of sequential convolution, recurrent, and fully connected blocks, was constructed. The CRNN was trained using the manually labelled images and then evaluated for accuracy using a first-look dataset. Sensitivity and positive predictive rates reached 81.6% and 87.9%, respectively. The predicted number and durations of scratching events correlated with those of the human observation. The trained CRNN could also successfully detect scratching in the hapten-induced atopic dermatitis mouse model (sensitivity, 94.8%; positive predictive rate, 82.1%). In conclusion, we established a novel scratching detection method using CRNN and showed that it can be used to study disease models.
Monkeys fight more in polluted air
Authors: Xu Aichun , Liu Chunhong , Wan Yue , Bai Yali , Li Zhongqiu
Published: January 2021

Air pollution is a global environmental problem, and its effects on human behavior, psychology, and health have been well studied. However, very few studies were done on if and how air pollution affects animal behavior, for example, social conflict. Many physiological and psychological evidences suggest a possible positive relationship between air pollution and animal social conflict, thus we established a multiple linear regression model using a captive monkey group to explore if monkeys behave more aggressively in polluted air. Our results confirmed that daily social fighting behaviors occurred more when air is polluted. Temperature has a nonlinear effect on monkey social conflict, with a fighting peak at 25–29 °C. To our knowledge, this is the first report that animal social conflict, like humans, is also affected by air pollution and temperature.
A record of vapour pressure deficit preserved in wood and soil across biomes
Authors: Broz Adrian , Retallack Gregory J. , Maxwell Toby M. , Silva Lucas C. R.
Published: January 2021

The drying power of air, or vapour pressure deficit (VPD), is an important measurement of potential plant stress and productivity. Estimates of VPD values of the past are integral for understanding the link between rising modern atmospheric carbon dioxide (pCO2) and global water balance. A geological record of VPD is needed for paleoclimate studies of past greenhouse spikes which attempt to constrain future climate, but at present there are few quantitative atmospheric moisture proxies that can be applied to fossil material. Here we show that VPD leaves a permanent record in the slope (S) of least-squares regressions between stable isotope ratios of carbon and oxygen (13C and 18O) found in cellulose and pedogenic carbonate. Using previously published data collected across four continents we show that S can be used to reconstruct VPD within and across biomes. As one application, we used S to estimate VPD of 0.46 kPa ± 0.26 kPa for cellulose preserved tens of millions of years ago—in the Eocene (45 Ma) Metasequoia from Axel Heiberg Island, Canada—and 0.82 kPa ± 0.52 kPa—in the Oligocene (26 Ma) for pedogenic carbonate from Oregon, USA—both of which are consistent with existing records at those locations. Finally, we discuss mechanisms that contribute to the positive correlation observed between VPD and S, which could help reconstruct past climatic conditions and constrain future alterations of global carbon and water cycles resulting from modern climate change.
Polymorphisms in Plasmodium falciparum dihydropteroate synthetase and dihydrofolate reductase genes in Nigerian children with uncomplicated malaria using high-resolution melting technique
Authors: Kayode Adeyemi T. , Ajogbasile Fehintola V. , Akano Kazeem , Uwanibe Jessica N. , Oluniyi Paul E. , Eromon Philomena J. , Folarin Onikepe A. , Sowunmi Akintunde , Wirth Dyann F. , Happi Christian T.
Published: January 2021

In 2005, the Nigerian Federal Ministry of Health revised the treatment policy for uncomplicated malaria with the introduction of artemisinin-based combination therapies (ACTs). This policy change discouraged the use of Sulphadoxine-pyrimethamine (SP) as the second-line treatment of uncomplicated falciparum malaria. However, SP is used as an intermittent preventive treatment of malaria in pregnancy (IPTp) and seasonal malaria chemoprevention (SMC) in children aged 3–59 months. There have been increasing reports of SP resistance especially in the non-pregnant population in Nigeria, thus, the need to continually monitor the efficacy of SP as IPTp and SMC by estimating polymorphisms in dihydropteroate synthetase (dhps) and dihydrofolate reductase (dhfr) genes associated with SP resistance. The high resolution-melting (HRM) assay was used to investigate polymorphisms in codons 51, 59, 108 and 164 of the dhfr gene and codons 437, 540, 581 and 613 of the dhps gene. DNA was extracted from 271 dried bloodspot filter paper samples obtained from children (< 5 years old) with uncomplicated malaria. The dhfr triple mutant I51R59N108, dhps double mutant G437G581 and quadruple dhfr I51R59N108 + dhps G437 mutant haplotypes were observed in 80.8%, 13.7% and 52.8% parasites, respectively. Although the quintuple dhfr I51R59N108 + dhps G437E540 and sextuple dhfr I51R59N108 + dhps G437E540G581 mutant haplotypes linked with in-vivo and in-vitro SP resistance were not detected, constant surveillance of these haplotypes should be done in the country to detect any change in prevalence.
Species sensitivity assessment of five Atlantic scleractinian coral species to 1-methylnaphthalene
Authors: Renegar D. Abigail , Turner Nicholas R.
Published: January 2021

Coral reefs are keystone coastal ecosystems that are at risk of exposure to petroleum from a range of sources, and are one of the highest valued natural resources for protection in Net Environmental Benefit Analysis (NEBA) in oil spill response. Previous research evaluating dissolved hydrocarbon impacts to corals reflected no clear characterization of sensitivity, representing an important knowledge gap in oil spill preparedness related to the potential impact of oil spills to the coral animal and its photosymbiont zooxanthellae. This research addresses this gap, using a standardized toxicity protocol to evaluate effects of a dissolved reference hydrocarbon on scleractinian corals. The relative sensitivity of five Atlantic scleractinian coral species to hydrocarbon exposure was assessed with 48-h assays using the reference polycyclic aromatic hydrocarbon 1-methylnaphthalene, based on physical coral condition, mortality, and photosynthetic efficiency. The threatened staghorn coral Acropora cervicornis was found to be the most sensitive to 1-methylnaphthalene exposure. Overall, the acute and subacute endpoints indicated that the tested coral species were comparatively more resilient to hydrocarbon exposure than other marine species. These results provide a framework for the prediction of oil spill impacts and impact thresholds on the coral animal and related habitats, essential for informing oil spill response in coastal tropical environments.
Familial Mediterranean fever-related miR-197-3p targets IL1R1 gene and modulates inflammation in monocytes and synovial fibroblasts
Authors: Akkaya-Ulum Yeliz Z. , Akbaba Tayfun Hilmi , Tavukcuoglu Zeynep , Chae Jae Jin , Yilmaz Engin , Ozen Seza , Balci-Peynircioglu Banu
Published: January 2021

Familial Mediterranean fever (FMF); is an autosomal recessively inherited autoinflammatory disease caused by the mutations in the Mediterranean Fever (MEFV) gene. Recent studies have shown that epigenetic control mechanisms, particularly non-coding RNAs, may play a role in the pathogenesis of autoinflammation. microRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating host gene expression at the post-transcriptional level. The phenotypic heterogeneity of FMF disease suggests that FMF may not be a monogenic disease, suggesting that epigenetic factors may affect phenotypic presentation. Here we examined the potential anti-inflammatory effect of miR-197-3p, which is a differentially expressed miRNA in FMF patients, by using inflammation related functional assays. We monitored gene expression levels of important cytokines, as well as performed functional studies on IL-1β secretion, caspase-1 activation, apoptosis assay, and cell migration assay. These experiments were used to evaluate the different stages of inflammation following pre-miR-197 transfection. Anti-miR-197 transfections were performed to test the opposite effect. 3′UTR luciferase activity assay was used for target gene studies. Our results obtained by inflammation-related functional assays demonstrated an anti-inflammatory effect of miR-197-3p in different cell types (synovial fibroblasts, monocytes, macrophages). 3′UTR luciferase activity assay showed that miR-197-3p directly binds to the interleukin-1beta (IL-1β) receptor, type I (IL1R1) gene, which is one of the key molecules of the inflammatory pathways. This study may contribute to understand the role of miR-197-3p in autoinflammation process. Defining the critical miRNAs may guide the medical community in a more personalized medicine in autoinflammatory diseases.
Intensity-dependent self-induced dual-color laser phase modulation and its effect on terahertz generation
Authors: Gong Chen , Kawayama Iwao , Murakami Hironaru , Teramoto Takahiro , Tonouchi Masayoshi
Published: January 2021

Powerful, broadband terahertz (THz) pulses and its application attract an exponential growth of interests. Dual-color laser filamentation in gases is one of the promising THz sources because of the scalability of the THz energy and wavelength with input parameters. But the additional phase induced by the nonlinearities associated with high intensities cannot be neglected because it may result in modulation of the THz waves. We investigate the influences of the infrared pump energy and air dispersion on the terahertz generation in dual-color laser filament. We observe that optimum dual-color laser relative phase of the THz generation undergoes a linear shift with increasing pump energy due to the intensity-induced refractive index change. This phase shift is verified by the spectral broadening of a two-color laser affected by the same mechanism. The result improves our understanding of the theoretical framework for a higher power THz source.
Quantitative assessment of pulmonary artery occlusion using lung dynamic perfusion CT
Authors: Jimenez-Juan Laura , Mehrez Hatem , Dey Chris , Homampour Shabnam , Salazar-Ferrer Pascal , Granton John T. , Lee Ting-Yim , Paul Narinder
Published: January 2021

Quantitative measurement of lung perfusion is a promising tool to evaluate lung pathophysiology as well as to assess disease severity and monitor treatment. However, this novel technique has not been adopted clinically due to various technical and physiological challenges; and it is still in the early developmental phase where the correlation between lung pathophysiology and perfusion maps is being explored. The purpose of this research work is to quantify the impact of pulmonary artery occlusion on lung perfusion indices using lung dynamic perfusion CT (DPCT). We performed Lung DPCT in ten anesthetized, mechanically ventilated juvenile pigs (18.6–20.2 kg) with a range of reversible pulmonary artery occlusions (0%, 40–59%, 60–79%, 80–99%, and 100%) created with a balloon catheter. For each arterial occlusion, DPCT data was analyzed using first-pass kinetics to derive blood flow (BF), blood volume (BV) and mean transit time (MTT) perfusion maps. Two radiologists qualitatively assessed perfusion maps for the presence or absence of perfusion defects. Perfusion maps were also analyzed quantitatively using a linear segmented mixed model to determine the thresholds of arterial occlusion associated with perfusion derangement. Inter-observer agreement was assessed using Kappa statistics. Correlation between arterial occlusion and perfusion indices was evaluated using the Spearman-rank correlation coefficient. Our results determined that perfusion defects were detected qualitatively in BF, BV and MTT perfusion maps for occlusions larger than 55%, 80% and 55% respectively. Inter-observer agreement was very good with Kappa scores > 0.92. Quantitative analysis of the perfusion maps determined the arterial occlusion threshold for perfusion defects was 50%, 76% and 44% for BF, BV and MTT respectively. Spearman-rank correlation coefficients between arterial occlusion and normalized perfusion values were strong (− 0.92, − 0.72, and 0.78 for BF, BV and MTT, respectively) and were statically significant (p < 0.01). These findings demonstrate that lung DPCT enables quantification and stratification of pulmonary artery occlusion into three categories: mild, moderate and severe. Severe (occlusion ≥ 80%) alters all perfusion indices; mild (occlusion < 55%) has no detectable effect. Moderate (occlusion 55–80%) impacts BF and MTT but BV is preserved.
Characterization of CHARK, an unusual cytokinin receptor of rice
Authors: Halawa Mhyeddeen , Cortleven Anne , Schmülling Thomas , Heyl Alexander
Published: January 2021

The signal transduction of the plant hormone cytokinin is mediated by a His-to-Asp phosphorelay. The canonical cytokinin receptor consists of an extra cytoplasmic hormone binding domain named cyclase/histidine kinase associated sensory extracellular (CHASE) and cytoplasmic histidine kinase and receiver domains. In addition to classical cytokinin receptors, a different type receptor—named CHASE domain receptor serine/threonine kinase (CHARK)—is also present in rice. It contains the same ligand binding domain as other cytokinin receptors but has a predicted Ser/Thr—instead of a His-kinase domain. Bioinformatic analysis indicates that CHARK is a retrogene and a product of trans-splicing. Here, we analyzed whether CHARK can function as a bona fide cytokinin receptor. A biochemical assay demonstrated its ability to bind cytokinin. Transient expression of CHARK in protoplasts increased their response to cytokinin. Expression of CHARK in an Arabidopsis receptor double mutant complemented its growth defects and restored the ability to activate cytokinin response genes, clearly demonstrating that CHARK functions as a cytokinin receptor. We propose that the CHARK gene presents an evolutionary novelty in the cytokinin signaling system.
Comparative transcriptome analysis reveals resistant and susceptible genes in tobacco cultivars in response to infection by Phytophthora nicotianae
Authors: Meng He , Sun Mingming , Jiang Zipeng , Liu Yutong , Sun Ying , Liu Dan , Jiang Caihong , Ren Min , Yuan Guangdi , Yu Wenlong , Feng Quanfu , Yang Aiguo , Cheng Lirui , Wang Yuanying
Published: January 2021

Phytophthora nicotianae is highly pathogenic to Solanaceous crops and is a major problem in tobacco production. The tobacco cultivar Beihart1000-1 (BH) is resistant, whereas the Xiaohuangjin 1025 (XHJ) cultivar is susceptible to infection. Here, BH and XHJ were used as models to identify resistant and susceptible genes using RNA sequencing (RNA-seq). Roots were sampled at 0, 6, 12, 24, and 60 h post infection. In total, 23,753 and 25,187 differentially expressed genes (DEGs) were identified in BH and XHJ, respectively. By mapping upregulated DEGs to the KEGG database, changes of the rich factor of “plant pathogen interaction pathway” were corresponded to the infection process. Of all the DEGs in this pathway, 38 were specifically regulated in BH. These genes included 11 disease-resistance proteins, 3 pathogenesis-related proteins, 4 RLP/RLKs, 2 CNGCs, 7 calcium-dependent protein kinases, 4 calcium-binding proteins, 1 mitogen-activated protein kinase kinase, 1 protein EDS1L, 2 WRKY transcription factors, 1 mannosyltransferase, and 1 calmodulin-like protein. By combining the analysis of reported susceptible (S) gene homologs and DEGs in XHJ, 9 S gene homologs were identified, which included 1 calmodulin-binding transcription activator, 1 cyclic nucleotide-gated ion channel, 1 protein trichome birefringence-like protein, 1 plant UBX domain-containing protein, 1 ADP-ribosylation factor GTPase-activating protein, 2 callose synthases, and 2 cellulose synthase A catalytic subunits. qRT-PCR was used to validate the RNA-seq data. The comprehensive transcriptome dataset described here, including candidate resistant and susceptible genes, will provide a valuable resource for breeding tobacco plants resistant to P. nicotianae infections.
Attentional focus modulates automatic finger-tapping movements
Authors: Zhang Xilei , Jiang Xingxun , Yuan Xiangyong , Zheng Wenming
Published: January 2021

The majority of human behaviors are composed of automatic movements (e.g., walking or finger-tapping) which are learned during nurturing and can be performed simultaneously without interfering with other tasks. One critical and yet to be examined assumption is that the attention system has the innate capacity to modulate automatic movements. The present study tests this assumption. Setting no deliberate goals for movement, we required sixteen participants to perform personalized and well-practiced finger-tapping movements in three experiments while focusing their attention on either different component fingers or away from movements. Using cutting-edge pose estimation techniques to quantify tapping trajectory, we showed that attention to movement can disrupt movement automaticity, as indicated by decreased inter-finger and inter-trial temporal coherence; facilitate the attended and inhibit the unattended movements in terms of tapping amplitude; and re-organize the action sequence into distinctive patterns according to the focus of attention. These findings demonstrate compelling evidence that attention can modulate automatic movements and provide an empirical foundation for theories based on such modulation in controlling human behavior.
Shedding light on the prefrontal correlates of mental workload in simulated driving: a functional near-infrared spectroscopy study
Authors: Geissler Christoph F. , Schneider Jörn , Frings Christian
Published: January 2021

Optimal mental workload plays a key role in driving performance. Thus, driver-assisting systems that automatically adapt to a drivers current mental workload via brain–computer interfacing might greatly contribute to traffic safety. To design economic brain computer interfaces that do not compromise driver comfort, it is necessary to identify brain areas that are most sensitive to mental workload changes. In this study, we used functional near-infrared spectroscopy and subjective ratings to measure mental workload in two virtual driving environments with distinct demands. We found that demanding city environments induced both higher subjective workload ratings as well as higher bilateral middle frontal gyrus activation than less demanding country environments. A further analysis with higher spatial resolution revealed a center of activation in the right anterior dorsolateral prefrontal cortex. The area is highly involved in spatial working memory processing. Thus, a main component of drivers’ mental workload in complex surroundings might stem from the fact that large amounts of spatial information about the course of the road as well as other road users has to constantly be upheld, processed and updated. We propose that the right middle frontal gyrus might be a suitable region for the application of powerful small-area brain computer interfaces.
Testing two competing hypotheses for Eurasian jays’ caching for the future
Authors: Amodio Piero , Brea Johanni , Farrar Benjamin G. , Ostojić Ljerka , Clayton Nicola S.
Published: January 2021

Previous research reported that corvids preferentially cache food in a location where no food will be available or cache more of a specific food in a location where this food will not be available. Here, we consider possible explanations for these prospective caching behaviours and directly compare two competing hypotheses. The Compensatory Caching Hypothesis suggests that birds learn to cache more of a particular food in places where that food was less frequently available in the past. In contrast, the Future Planning Hypothesis suggests that birds recall the ‘what–when–where’ features of specific past events to predict the future availability of food. We designed a protocol in which the two hypotheses predict different caching patterns across different caching locations such that the two explanations can be disambiguated. We formalised the hypotheses in a Bayesian model comparison and tested this protocol in two experiments with one of the previously tested species, namely Eurasian jays. Consistently across the two experiments, the observed caching pattern did not support either hypothesis; rather it was best explained by a uniform distribution of caches over the different caching locations. Future research is needed to gain more insight into the cognitive mechanism underpinning corvids’ caching for the future.
Impact of low-frequency coding variants on human facial shape
Authors: Liu Dongjing , Alhazmi Nora , Matthews Harold , Lee Myoung Keun , Li Jiarui , Hecht Jacqueline T. , Wehby George L. , Moreno Lina M. , Heike Carrie L. , Roosenboom Jasmien , Feingold Eleanor , Marazita Mary L. , Claes Peter , Liao Eric C. , Weinberg Seth M. , Shaffer John R.
Published: January 2021

The contribution of low-frequency variants to the genetic architecture of normal-range facial traits is unknown. We studied the influence of low-frequency coding variants (MAF < 1%) in 8091 genes on multi-dimensional facial shape phenotypes in a European cohort of 2329 healthy individuals. Using three-dimensional images, we partitioned the full face into 31 hierarchically arranged segments to model facial morphology at multiple levels, and generated multi-dimensional phenotypes representing the shape variation within each segment. We used MultiSKAT, a multivariate kernel regression approach to scan the exome for face-associated low-frequency variants in a gene-based manner. After accounting for multiple tests, seven genes (AR, CARS2, FTSJ1, HFE, LTB4R, TELO2, NECTIN1) were significantly associated with shape variation of the cheek, chin, nose and mouth areas. These genes displayed a wide range of phenotypic effects, with some impacting the full face and others affecting localized regions. The missense variant rs142863092 in NECTIN1 had a significant effect on chin morphology and was predicted bioinformatically to have a deleterious effect on protein function. Notably, NECTIN1 is an established craniofacial gene that underlies a human syndrome that includes a mandibular phenotype. We further showed that nectin1a mutations can affect zebrafish craniofacial development, with the size and shape of the mandibular cartilage altered in mutant animals. Findings from this study expanded our understanding of the genetic basis of normal-range facial shape by highlighting the role of low-frequency coding variants in several novel genes.