bluuebunny/crossref_metadata_2025 huggingface dataset:
Surface Energy Partitioning and Evaporative Fraction in a Water-Saving Irrigated Rice Field
Authors: Liu Xiaoyin , Xu Junzeng , Yang Shihong , Lv Yuping
Published: January 2019

Surface energy distribution in paddy fields and the ratio of latent heat flux (LE) to available energy, termed as the evaporative fraction (EF), are essential for an understanding of water and energy processes. They are expected to vary in different ways in response to changes in the soil moisture condition under water-saving irrigation practice. In this study, the diurnal and seasonal variations in energy distribution were examined based on the data measured by the eddy covariance system and corrected with enforcing energy balance closure by the EF method in water-saving irrigated rice paddies in 2015 and 2016. Soil heat flux (G) values were similar in magnitude to sensible heat flux (Hs) values, with both accounting for approximately 5% of the energy input. Both magnitudes of G and Hs were significantly lower than that of LE. Generally, EF in water-saving irrigated rice paddies was larger than that of other ecosystems, and varied within a narrow range from 0.7 to 1.0. Diurnally, EF decreased till noon and then increased slowly in the afternoon till sunset. It was found be less varied between 10:00 and 14:00. Seasonally, the alternative drying-wetting soil water conditions in water-saving irrigated rice paddies resulted in a change in the variation of the EF. The LE flux is the largest component of available energy, with EF being mostly higher than 0.9. EF, increasing consistently till the tillering stage, remaining high from the late tillering to milk stage, and then following a declining trend. The maximum EF (approaching 1.0) was found in the milk stage. The results of EF in water-saving irrigated rice paddies will be helpful for estimating daily or long temporal scale evapotranspiration (ET) by the EF method based on satellite-derived ET.
Robust Nocturnal and Early Morning Summer Rainfall Peaks over Continental East Asia in a Global Multiscale Modeling Framework
Authors: Zhang Yi , Chen Haoming , Wang Dan
Published: January 2019

The diurnal cycle of convection and precipitation is an important atmospheric feature. It also poses a great challenge to global numerical atmospheric modeling. Over continental East Asia, most global models cannot well capture the nocturnal and early morning peaks of summer rainfall. This problem may lead to dry biases and limit the modeling skills. This study investigates this problem using a global multiscale modeling framework (Super-Parameterized CAM5; SPCAM5). The nocturnal and early morning peaks, which are almost absent in CAM5 and a coarser-resolution SPCAM5, can be successfully captured by SPCAM5 with a moderate increase in the horizontal resolution. On the lee side of the Tibetan Plateau, SPCAM5 generates robust eastward propagating rainfall signals, which correspond to the moving convective systems, as revealed by the heating and drying profiles. Over the eastern plain of China, the early morning peaks become more evident, corresponding to a stratiform-type heating structure in the midlevel. A sensitivity experiment with altered grid-scale forcing also suggests the important preconditioning role of the vertical moisture advection in regulating the early morning peaks. These results highlight the added value of representing multiscale processes to the successful simulation of the diurnal cycle over continental East Asia.
Quantum Rainbows in Positron Transmission through Carbon Nanotubes
Authors: Ćosić Marko , Petrović Srđan , Nešković Nebojša
Published: January 2019

Here we report the results of the theoretical investigation of the transmission of channeled positrons through various short chiral single walled carbon nanotubes (SWCNT). The main question answered by this study is “What are the manifestations of the rainbow effect in the channeling of quantum particles that happens during the channeling of classical particles?” To answer this question, the corresponding classical and quantum problems were solved in parallel, critically examined, and compared with each other. Positron energies were taken to be 1 MeV when the quantum approach was necessary. The continuum positron-nanotube potential was constructed from the thermally averaged Molière’s positron-carbon potential. In the classical approach, a positron beam is considered as an ensemble of noninteracting particles. In the quantum approach, it is considered as an ensemble of noninteracting wave packages. Distributions of transmitted positrons were constructed from the numerical solutions of Newton’s equation and the time-dependent Schrödinger equation. For the transmission of 1-MeV positrons through 200-nm long SWCNT (14; 4), in addition to the central maximum, the quantum angular distribution has a prominent peak pair (close to the classical rainbows) and two smaller peaks pairs. We have shown that even though the semiclassical approximation is not strictly applicable it is useful for explanation of the observed behavior. In vicinity of the most prominent peak, i.e., the primary rainbow peak, rays interfere constructively. On one of its sides, rays become complex, which explains the exponential decay of the probability density in that region. On the other side, the ray interference alternates between constructive and destructive, thus generating two observed supernumerary rainbow peaks. The developed model was then applied for the explanation of the angular distributions of 1-MeV positrons transmitting through 200 nm long (7, 3), (8, 5), (9, 7), (14, 4), (16, 5) and (17, 7) SWCNTs. It has been shown that this explains most but not all rainbow patterns. Therefore, a new method for the identification and classification of quantum rainbows was developed relying only on the morphological properties of the positron wave function amplitude and the phase function families. This led to a detailed explanation of the way the quantum rainbows are generated. All wave packets wrinkle due to their internal focusing in a mutually coordinated way and are concentrated near the position of the corresponding classical rainbow. This explanation is general and applicable to the investigations of quantum effects occurring in various other atomic collision processes.
Impaired CENP-E Function Renders Large Chromosomes More Vulnerable to Congression Failure
Authors: Tovini Laura , McClelland Sarah E.
Published: January 2019

It has recently emerged that human chromosomes vary between one another in terms of features that impact their behaviour during impaired chromosome segregation, leading to non-random aneuploidy in the daughter cell population. During the process of chromosome congression to the metaphase plate, chromosome movement is guided by kinesin-like proteins, among which centromere-associated protein E (CENP-E) is important to transport chromosomes along the microtubules of the mitotic spindle. It is known that the inhibition of CENP-E notably impairs alignment for a subset of chromosomes, particularly those positioned close to the centrosome at nuclear envelope breakdown (‘polar chromosomes’); it is, however, not clear whether chromosome identity could influence this process. Since a popular strategy to model aneuploidy is to induce congression defects (for example combining CENP-E inhibitors with mitotic checkpoint abrogation), variance in congression efficiency between chromosomes might influence the landscape of aneuploidy and subsequent cell fates. By combining immunofluorescence, live cell imaging and fluorescence in situ hybridisation, we investigated the behaviour of polar chromosomes and their dependency upon CENP-E-mediated congression in human cells. We observed a bias in congression efficiency related to chromosome size, with larger chromosomes more sensitive to CENP-E inhibition. This bias is likely due to two contributing factors; an initial propensity of larger chromosomes to be peripheral and thus rely more upon CENP-E function to migrate to the metaphase plate, and additionally a bias between specific chromosomes’ ability to congress from a polar state. These findings may help to explain the persistence of a subset of chromosomes at the centrosome following CENP-E disruption, and also have implications for the spectrum of aneuploidy generated following treatments to manipulate CENP-E function.
Anti-Tumor Activity of Cembranoid-Type Diterpenes Isolated from Nicotiana tabacum L.
Authors: Yuan Xiao-Long , Mao Xin-Xin , Du Yong-Mei , Yan Pei-Zhen , Hou Xiao-Dong , Zhang Zhong-Feng
Published: January 2019

Recently, the incidence of hepatocellular carcinoma has increased worldwide. Cembranoid-type diterpenes (CBDs) from tobacco exhibit good antimicrobial, antitumor, and neuroprotective activities. Therefore, in this study, we isolated CBDs from Nicotiana tabacum L. and evaluated their antitumor activity against hepatoma cell lines. Particularly, the anti-tumor activity of α-2,7,11-cyprotermine-4,6-diol (α-CBD) was investigated against HepG2, SMMC-7721, and HL-7702 cells. The MTT assay revealed that α-CBD reduced the formation of cell clones and inhibited the proliferation of hepatocellular carcinoma cells. Morphological observations showed that α-CBD altered cell morphology and membrane permeability before inducing apoptosis. To further explore the antitumor mechanism of α-CBD, flow cytometry and transcriptome analysis were performed using HepG2 cells. The results showed that the number of HepG2 cells increased from 10.4% to 29.8%, indicating that α-CBD inhibits the proliferation of hepatocellular carcinoma cells in the S phase. The gene expression analysis of HepG2 cells treated with α-CBD showed 3068 genes with altered expression, among which 1289 were upregulated and 1779 were downregulated. Apoptosis induced by these differentially expressed genes might be mediated by the p53-PUMA, PI3K-Akt, and IL-1-NF-κB-IAP pathways. Comprehensively, our study shows that α-CBD isolated from N. tabacum L. can be potentially used as a natural antitumor agent.
A Biophysical Approach to the Identification of Novel ApoE Chemical Probes
Authors: Kraft Lucas , Serpell Louise C. , Atack John R.
Published: January 2019

Alzheimer’s disease (AD) is the most common type of dementia and, after age, the greatest risk factor for developing AD is the allelic variation of apolipoprotein E (ApoE), with homozygote carriers of the ApoE4 allele having an up to 12-fold greater risk of developing AD than noncarriers. Apolipoprotein E exists as three isoforms that differ in only two amino acid sites, ApoE2 (Cys112/Cys158), ApoE3 (Cys112/Arg158), and ApoE4 (Arg112/Arg158). These amino acid substitutions are assumed to alter ApoE structure and function, and be responsible for the detrimental effects of ApoE4 via a mechanism that remains unclear. The hypothesis that a structural difference between ApoE4 and ApoE3 (and ApoE2) is the cause of the ApoE4-associated increased risk for AD forms the basis of a therapeutic approach to modulate ApoE4 structure, and we were therefore interested in screening to identify new chemical probes for ApoE4. In this regard, a high-yield protocol was developed for the expression and purification of recombinant full-length ApoE, and three diverse biophysical screening assays were established and characterized; an optical label-free assay (Corning Epic) for hit identification and microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) as orthogonal assays for hit confirmation. The 707 compounds in the National Institute of Health clinical collection were screened for binding to ApoE4, from which six confirmed hits, as well as one analogue, were identified. Although the compounds did not differentiate between ApoE isoforms, these data nevertheless demonstrate the feasibility of using a biophysical approach to identifying compounds that bind to ApoE and that, with further optimization, might differentiate between isoforms to produce a molecule that selectively alters the function of ApoE4.
Analyzing Moment Arm Profiles in a Full-Muscle Rat Hindlimb Model
Authors: Young Fletcher , Rode Christian , Hunt Alex , Quinn Roger
Published: January 2019

Understanding the kinematics of a hindlimb model is a fundamental aspect of modeling coordinated locomotion. This work describes the development process of a rat hindlimb model that contains a complete muscular system and incorporates physiological walking data to examine realistic muscle movements during a step cycle. Moment arm profiles for selected muscles are analyzed and presented as the first steps to calculating torque generation at hindlimb joints. A technique for calculating muscle moment arms from muscle attachment points in a three-dimensional (3D) space has been established. This model accounts for the configuration of adjacent joints, a critical aspect of biarticular moment arm analysis that must be considered when calculating joint torque. Moment arm profiles from isolated muscle motions are compared to two existing models. The dependence of biarticular muscle’s moment arms on the configuration of the adjacent joint is a critical aspect of moment arm analysis that must be considered when calculating joint torque. The variability in moment arm profiles suggests changes in muscle function during a step.
A Molecular Interaction Analysis Reveals the Possible Roles of Graphene Oxide in a Glucose Biosensor
Authors: Sumaryada Tony , Sandy Gunawan Muhammad , Perdana Salahuddin , Arjo Sugianto , Maddu Akhiruddin
Published: January 2019

In this paper, we report the molecular docking study of graphene oxide and glucose oxidase (GOx) enzyme for a potential glucose biosensing application. The large surface area and good electrical properties have made graphene oxide as one of the best candidates for an enzyme immobilizer and transducer in the biosensing system. Our molecular docking results revealed that graphene oxide plays a role as a GOx enzyme immobilizer in the glucose biosensor system since it can spontaneously bind with GOx at specific regions separated from the active sites of glucose and not interfering or blocking the glucose sensing by GOx in an enzyme-assisted biosensor system. The strongest binding affinity of GOx-graphene oxide interaction is −11.6 kCal/mol and dominated by hydrophobic interaction. Other modes of interactions with a lower binding affinity have shown the existence of some hydrogen bonds (H-bonds). A possibility of direct sensing (interaction) model of glucose by graphene oxide (non-enzymatic sensing mechanism) was also studied in this paper, and showed a possible direct glucose sensing by graphene oxide through the H-bond interaction, even though with a much lower binding affinity of −4.2 kCal/mol. It was also found that in a direct glucose sensing mechanism, the sensing interaction can take place anywhere on the graphene oxide surface with almost similar binding affinity.
Electrical Brain Responses Reveal Sequential Constraints on Planning during Music Performance
Authors: Mathias Brian , Gehring William J. , Palmer Caroline
Published: January 2019

Elements in speech and music unfold sequentially over time. To produce sentences and melodies quickly and accurately, individuals must plan upcoming sequence events, as well as monitor outcomes via auditory feedback. We investigated the neural correlates of sequential planning and monitoring processes by manipulating auditory feedback during music performance. Pianists performed isochronous melodies from memory at an initially cued rate while their electroencephalogram was recorded. Pitch feedback was occasionally altered to match either an immediately upcoming Near-Future pitch (next sequence event) or a more distant Far-Future pitch (two events ahead of the current event). Near-Future, but not Far-Future altered feedback perturbed the timing of pianists’ performances, suggesting greater interference of Near-Future sequential events with current planning processes. Near-Future feedback triggered a greater reduction in auditory sensory suppression (enhanced response) than Far-Future feedback, reflected in the P2 component elicited by the pitch event following the unexpected pitch change. Greater timing perturbations were associated with enhanced cortical sensory processing of the pitch event following the Near-Future altered feedback. Both types of feedback alterations elicited feedback-related negativity (FRN) and P3a potentials and amplified spectral power in the theta frequency range. These findings suggest similar constraints on producers’ sequential planning to those reported in speech production.
Potential Application of Optogenetic Stimulation in the Treatment of Pain and Migraine Headache: A Perspective from Animal Studies
Authors: Liu Sufang , Tang Yuanyuan , Xing Ying , Kramer Phillip , Bellinger Larry , Tao Feng
Published: January 2019

Optogenetic manipulation is uniquely useful in unraveling the functional organization of neuronal circuits in the central nervous system by enabling reversible gain- or loss-of-function of discrete populations of neurons within restricted brain regions. This state-of-the-art technology can produce circuit-specific neuromodulation by overexpressing light-sensitive proteins (opsins) in particular cell types of interest. Here, we discuss the principle of optogenetic manipulation and its application in pain research using animal models, and we also discuss how to potentially use optogenetic stimulation in the treatment of migraine headache in the future.
A Pilot Quantitative Evaluation of Early Life Language Development in Fragile X Syndrome
Authors: Reisinger Debra L. , Shaffer Rebecca C. , Pedapati Ernest V. , Dominick Kelli C. , Erickson Craig A.
Published: January 2019

Language delay and communication deficits are a core characteristic of the fragile X syndrome (FXS) phenotype. To date, the literature examining early language development in FXS is limited potentially due to barriers in language assessment in very young children. The present study is one of the first to examine early language development through vocal production and the language learning environment in infants and toddlers with FXS utilizing an automated vocal analysis system. Child vocalizations, conversational turns, and adult word counts in the home environment were collected and analyzed in a group of nine infants and toddlers with FXS and compared to a typically developing (TD) normative sample. Results suggest infants and toddlers with FXS are exhibiting deficits in their early language skills when compared to their chronological expectations. Despite this, when accounting for overall developmental level, their early language skills appear to be on track. Additionally, FXS caregivers utilize less vocalizations around infants and toddlers with FXS; however, additional research is needed to understand the true gap between FXS caregivers and TD caregivers. These findings provide preliminary information about the early language learning environment and support for the feasibility of utilizing an automated vocal analysis system within the FXS population that could ease data collection and further our understanding of the emergence of language development.
On the Relationship between P3 Latency and Mental Ability as a Function of Increasing Demands in a Selective Attention Task
Authors: Kapanci Tugba , Merks Sarah , Rammsayer Thomas H. , Troche Stefan J.
Published: January 2019

The mental speed approach to individual differences in mental ability (MA) is based on the assumption of higher speed of information processing in individuals with higher than those with lower MA. Empirical support of this assumption has been inconsistent when speed was measured by means of the P3 latency in the event-related potential (ERP). The present study investigated the association between MA and P3 latency as a function of task demands on selective attention. For this purpose, 20 men and 90 women performed on a standard continuous performance test (CPT1 condition) as well as on two further task conditions with lower (CPT0) and higher demands (CPT2) on selective attention. MA and P3 latency negatively correlated in the standard CPT, and this negative relationship even increased systematically from the CPT1 to the CPT2 condition but was absent in the CPT0 condition. The present results indicate that task demands on selective attention are decisive to observe the expected shorter P3 latency in individuals with higher compared to those with lower MA.
Sense of Coherence and Caregivers of Persons with Dementia
Authors: Childers Kristina M.
Published: January 2019

Unpaid caregivers (CG) provide most of the assistance to persons with dementias (PWD) living in the community. This study explores the current state of knowledge regarding the concept of sense of coherence (SOC) and CG of PWD via a concept analysis. The identified defining attributes were health, health-related quality of life (HRQoL), CG burden, CG stress, coping as a strength, gender, and decreasing sense of CG coherence over the progression of the disease (dementia). Further study by health care professionals using clinical observations, large samples of respondents, a consistent theory, valid and reliable instruments used to measure defining attributes consistently, and critical reviews of the literature are needed.
Cognitive Behavioral Therapy (CBT) in Psychogenic Non-Epileptic Seizures (PNES): A Case Report and Literature Review
Authors: Kamil Saher Hoda , Qureshi Mustafa , Patel Rikinkumar S.
Published: January 2019

Psychogenic non-epileptic seizures (PNES) are classified as a somatoform conversion disorder. We present a case of a 24-year-old male with a past psychiatric history of posttraumatic stress disorder (PTSD) and anxiety disorder, admitted to our inpatient psychiatric unit. The patient experienced multiple episodes of seizures during hospitalization. Work up was unremarkable, and PNES were suspected and later confirmed with video-electroencephalography (video-EEG). He underwent supervised withdrawal of antiepileptic medications with the initiation of cognitive behavioral therapy (CBT), which reduced the frequency of seizures. Diagnosis of PNES can present as a challenge and failure to diagnose its psychological nature can lead to a delay in the psychological intervention. CBT leads to a decrease in seizure frequency, and improvement in psychiatric symptoms, psychosocial functioning, and quality of life. It is important to consider PNES in the differential diagnosis of seizures presented by psychiatric patients, as CBT is necessary for better patient outcomes.
Education Attainment and Obesity：Differential Returns Based on Sexual Orientation
Authors: Assari Shervin
Published: January 2019

Background: Although high educational attainment is linked to better health and lower health risk behaviors, this effect may be systemically smaller for racial and ethnic minority groups compared to Whites. However, it is still unknown whether these diminished returns also apply to marginalization based on sexual orientation. Aims: In a national sample of adults which was composed of people of color, we compared straight and homosexual people for the association between education attainment and obesity. Methods: The Social Justice Sexuality Project (SJS-2010) is a cross-sectional national survey of health and wellbeing of predominantly people of color who identify as homosexual. The current analysis included 2884 adults (age 24 or more) who were either heterosexual (n = 260) or homosexual (n = 2624). The predictor variable was education attainment, and the outcome variable was obesity status (body mass index larger than 30 kg/m2 [kilograms per meter squared]). Demographic factors (age and gender), household income, nativity (US born vs. immigrant), and health (self-rated health and current smoking) were the covariates. Sexual orientation was the moderator. Results: In the pooled sample, high education attainment was protective against obesity status. Sexual orientation interacted with education attainment on odds of obesity, which was suggestive of stronger protective effects of high education attainment against obesity for heterosexual than homosexual individuals. Conclusion: High education attainment better protects heterosexual than homosexual people against obesity, a pattern similar to what has been observed for comparison of Whites and non-Whites. Smaller protective effects of education attainment on health behaviors of marginalized people are possibly, due to prejudice and discrimination that they experience. Discrimination may minimize stigmatized individuals’ abilities to mobilize their economic and human resources and translate them to tangible outcomes. This finding extends the Minorities’ Diminished Returns theory, suggesting that it is not just race/ethnicity but possibly any marginalizing and stigmatizing social identity that results in diminished returns of socioeconomic status resources.
Locating Hidden Elements in Walls of Cultural Heritage Buildings by Using Infrared Thermography
Authors: Glavaš Hrvoje , Hadzima-Nyarko Marijana , Haničar Buljan Ivana , Barić Tomislav
Published: January 2019

The structure of Tvrđa and its buildings date back to the Middle Ages. Tvrđa represents the Old Town of the city of Osijek and the best-preserved and largest ensemble of Baroque buildings in Croatia. After the withdrawal of the Ottomans in 1687, during the 18th century, the Austro-Hungarian administration systematically formed a new fortification system, regulated streets and squares and built a large number of military objects. Tvrđa took its present form in the 19th century and has kept it since then. Investigating the historical development of individual buildings, in addition to archival sources and existing architectural documentation, the obvious source of information are the buildings themselves. The aim of this paper is to explore the possibilities of using infrared thermography to find structural elements and hidden openings in historic buildings in Osijek’s Tvrđa. This paper describes the exploration of the 18th century openings on the facades of the former Kostić houses. The facades were bricked into the walls in the 19th century because houses were reused and their purposes changed from commercial to residential. Infrared thermography is often a starting, nondestructive testing method (NDT) for building analyses. This paper presents thermographic analyses of two buildings. The analyses were carried out in December 2017 and January 2018. Using a steady-state thermographic analysis of a building envelope as the first step, the audit was continued with step heating (SH) of an interest point where changes in a thermal pattern were expected due to additional bricking. Heat flux was generated by the usage of a heat gun for paint removal.
MiR-657/ATF2 Signaling Pathway Has a Critical Role in Spatholobus suberectus Dunn Extract-Induced Apoptosis in U266 and U937 Cells
Authors: Lim Hyun Ji , Park Moon Nyeo , Kim Changmin , Kang Beomku , Song Hyo-Sook , Lee Hyemin , Kim Sung-Hoon , Shim Bum-Sang , Kim Bonglee
Published: January 2019

Though Spatholobus suberectus Dunn (SSD) has been reported to have anti-virus, anti-osteoclastogenesis, and anti-inflammation activities, its underlying anti-cancer mechanism has never been elucidated in association with the role of miR-657 in endoplasmic reticulum (ER) stress-related apoptosis to date. SSD treatment exerted cytotoxicity in U266 and U937 cells in a dose-dependent manner. Also, apoptosis-related proteins such as PARP, procaspase-3, and Bax were regulated by SSD treatment. Furthermore, Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay revealed that a number of apoptotic bodies were increased by SSD. Interestingly, the ER stress-related proteins such as p-ATF2 and CHOP were elevated by SSD. Interestingly, reactive oxygen species (ROS) generation and cytotoxicity by SSD treatment were significantly reduced by N-Acetyl-L-cysteine (NAC). Among the microRNAs (miRNAs) regulated by SSD treatment, miR-657 was most significantly reduced by SSD treatment. However, an miR-657 mimic reversed SSD-induced apoptosis by the attenuation of the expression of p-ATF2, CHOP, and PARP cleavage. Overall, these findings provide scientific evidence that miR657 is an onco-miRNA targeting the ER stress signal pathway and SSD induces apoptosis via the inhibition of miR-657, ROS, and the activation of p-ATF2 and CHOP as a potent anti-cancer agent for myeloid-originated hematological cancer.
Combined Amino Acid Positron Emission Tomography and Advanced Magnetic Resonance Imaging in Glioma Patients
Authors: Lohmann Philipp , Werner Jan-Michael , Shah N. Jon , Fink Gereon R. , Langen Karl-Josef , Galldiks Norbert
Published: January 2019

Imaging techniques such as positron emission tomography (PET) and magnetic resonance imaging (MRI) provide valuable information about brain tumor patients. Particularly amino acid PET, advanced MRI techniques, and combinations thereof are of great interest for the non-invasive assessment of biological characteristics in patients with primary or secondary brain cancer. A methodological innovation that potentially advances research in patients with brain tumors is the increasing availability of hybrid PET/MRI systems, which enables the simultaneous acquisition of both imaging modalities. Furthermore, the advent of ultra-high field MRI scanners operating at magnetic field strengths of 7 T or more will allow further development of metabolic MR imaging at higher resolution. This review focuses on the combination of amino acid PET with MR spectroscopic imaging, perfusion- and diffusion-weighted imaging, as well as chemical exchange saturation transfer in patients with high-grade gliomas, especially glioblastomas.
An Integrative Data Mining and Omics-Based Translational Model for the Identification and Validation of Oncogenic Biomarkers of Pancreatic Cancer
Authors: Long Nguyen Phuoc , Jung Kyung Hee , Anh Nguyen Hoang , Yan Hong Hua , Nghi Tran Diem , Park Seongoh , Yoon Sang Jun , Min Jung Eun , Kim Hyung Min , Lim Joo Han , Kim Joon Mee , Lim Johan , Lee Sanghyuk , Hong Soon-Sun , Kwon Sung Won
Published: January 2019

Substantial alterations at the multi-omics level of pancreatic cancer (PC) impede the possibility to diagnose and treat patients in early stages. Herein, we conducted an integrative omics-based translational analysis, utilizing next-generation sequencing, transcriptome meta-analysis, and immunohistochemistry, combined with statistical learning, to validate multiplex biomarker candidates for the diagnosis, prognosis, and management of PC. Experiment-based validation was conducted and supportive evidence for the essentiality of the candidates in PC were found at gene expression or protein level by practical biochemical methods. Remarkably, the random forests (RF) model exhibited an excellent diagnostic performance and LAMC2, ANXA2, ADAM9, and APLP2 greatly influenced its decisions. An explanation approach for the RF model was successfully constructed. Moreover, protein expression of LAMC2, ANXA2, ADAM9, and APLP2 was found correlated and significantly higher in PC patients in independent cohorts. Survival analysis revealed that patients with high expression of ADAM9 (Hazard ratio (HR)OS = 2.2, p-value < 0.001), ANXA2 (HROS = 2.1, p-value < 0.001), and LAMC2 (HRDFS = 1.8, p-value = 0.012) exhibited poorer survival rates. In conclusion, we successfully explore hidden biological insights from large-scale omics data and suggest that LAMC2, ANXA2, ADAM9, and APLP2 are robust biomarkers for early diagnosis, prognosis, and management for PC.
Bleached Wood Supports for Floatable, Recyclable, and Efficient Three Dimensional Photocatalyst
Authors: He Yuming , Li Huayang , Guo Xuelian , Zheng Rongbo
Published: January 2019

To suppress the agglomeration of a photocatalyst, facilitate its recovery, and avoid photolysis of dyes, various support materials such as ceramic, carbon, and polymer have been investigated. However, these support materials pose the following additional challenges: ceramic supports will settle down at the bottom of their container due to their high density, while the carbon support will absorb the UV-vis light for its black color. Herein, we propose a floatable, UV transmitting, mesoporous bleached wood with most lignin removal to support P25 nanoparticles (BP-wood) that can effectively, recyclable, three dimensional (3D) photocatalytic degrade dyes such as methylene blue (MB) under ambient sunlight. The BP-wood has the following advantages: (1) The delignification makes the BP-wood more porous to not only quickly transport MB solutions upstream to the top surface, but is also decorated with P25 nanoparticles on the cell wall to form a 3D photocatalyst. (2) The delignification endows the BP-wood with good UV transmittance to undergo 3D photocatalytic degradation under sunlight. (3) It can float on the surface of the MB solution to capture more sunlight to enhance the photodegradation efficiency by suppressing the photolysis of MB. (4) It has comparable or even better photocatalytic degradation of 40 mg/L and 60 mg/L MB than that of P25 nanoparticles suspension. (5) It is green, recyclable, and scalable.
Implications and Current Limitations of Oogenesis from Female Germline or Oogonial Stem Cells in Adult Mammalian Ovaries
Authors: Martin Jessica J. , Woods Dori C. , Tilly Jonathan L.
Published: January 2019

A now large body of evidence supports the existence of mitotically active germ cells in postnatal ovaries of diverse mammalian species, including humans. This opens the possibility that adult stem cells naturally committed to a germline fate could be leveraged for the production of female gametes outside of the body. The functional properties of these cells, referred to as female germline or oogonial stem cells (OSCs), in ovaries of women have recently been tested in various ways, including a very recent investigation of the differentiation capacity of human OSCs at a single cell level. The exciting insights gained from these experiments, coupled with other data derived from intraovarian transplantation and genetic tracing analyses in animal models that have established the capacity of OSCs to generate healthy eggs, embryos and offspring, should drive constructive discussions in this relatively new field to further exploring the value of these cells to the study, and potential management, of human female fertility. Here, we provide a brief history of the discovery and characterization of OSCs in mammals, as well as of the in-vivo significance of postnatal oogenesis to adult ovarian function. We then highlight several key observations made recently on the biology of OSCs, and integrate this information into a broader discussion of the potential value and limitations of these adult stem cells to achieving a greater understanding of human female gametogenesis in vivo and in vitro.
Large-Scale Assessment of Bioinformatics Tools for Lysine Succinylation Sites
Authors: Hasan Md. Mehedi , Khatun Mst. Shamima , Kurata Hiroyuki
Published: January 2019

Lysine succinylation is a form of posttranslational modification of the proteins that play an essential functional role in every aspect of cell metabolism in both prokaryotes and eukaryotes. Aside from experimental identification of succinylation sites, there has been an intense effort geared towards the development of sequence-based prediction through machine learning, due to its promising and essential properties of being highly accurate, robust and cost-effective. In spite of these advantages, there are several problems that are in need of attention in the design and development of succinylation site predictors. Notwithstanding of many studies on the employment of machine learning approaches, few articles have examined this bioinformatics field in a systematic manner. Thus, we review the advancements regarding the current state-of-the-art prediction models, datasets, and online resources and illustrate the challenges and limitations to present a useful guideline for developing powerful succinylation site prediction tools.
Impairment of Motor Function Correlates with Neurometabolite and Brain Iron Alterations in Parkinson’s Disease
Authors: Pesch Beate , Casjens Swaantje , Woitalla Dirk , Dharmadhikari Shalmali , Edmondson David A. , Zella Maria Angela Samis , Lehnert Martin , Lotz Anne , Herrmann Lennard , Muhlack Siegfried , Kraus Peter , Yeh Chien-Lin , Glaubitz Benjamin , Schmidt-Wilcke Tobias , Gold Ralf , van Thriel Christoph , Brüning Thomas , Tönges Lars , Dydak Ulrike
Published: January 2019

We took advantage of magnetic resonance imaging (MRI) and spectroscopy (MRS) as non-invasive methods to quantify brain iron and neurometabolites, which were analyzed along with other predictors of motor dysfunction in Parkinson’s disease (PD). Tapping hits, tremor amplitude, and the scores derived from part III of the Movement Disorder Society-Sponsored Revision of the Unified Parkinson Disease Rating Scale (MDS-UPDRS3 scores) were determined in 35 male PD patients and 35 controls. The iron-sensitive MRI relaxation rate R2* was measured in the globus pallidus and substantia nigra. γ-aminobutyric acid (GABA)-edited and short echo-time MRS was used for the quantification of neurometabolites in the striatum and thalamus. Associations of R2*, neurometabolites, and other factors with motor function were estimated with Spearman correlations and mixed regression models to account for repeated measurements (hands, hemispheres). In PD patients, R2* and striatal GABA correlated with MDS-UPDRS3 scores if not adjusted for age. Patients with akinetic-rigid PD subtype (N = 19) presented with lower creatine and striatal glutamate and glutamine (Glx) but elevated thalamic GABA compared to controls or mixed PD subtype. In PD patients, Glx correlated with an impaired dexterity when adjusted for covariates. Elevated myo-inositol was associated with more tapping hits and lower MDS-UPDRS3 scores. Our neuroimaging study provides evidence that motor dysfunction in PD correlates with alterations in brain iron and neurometabolites.
Targeting Hedgehog Signalling through the Ubiquitylation Process: The Multiple Roles of the HECT-E3 Ligase Itch
Authors: Infante Paola , Lospinoso Severini Ludovica , Bernardi Flavia , Bufalieri Francesca , Di Marcotullio Lucia
Published: January 2019

Hedgehog signalling (Hh) is a developmental conserved pathway strongly involved in cancers when deregulated. This important pathway is orchestrated by numerous regulators, transduces through distinct routes and is finely tuned at multiple levels. In this regard, ubiquitylation processes stand as essential for controlling Hh pathway output. Although this post-translational modification governs proteins turnover, it is also implicated in non-proteolytic events, thereby regulating the most important cellular functions. The HECT E3 ligase Itch, well known to control immune response, is emerging to have a pivotal role in tumorigenesis. By illustrating Itch specificities on Hh signalling key components, here we review the role of this HECT E3 ubiquitin ligase in suppressing Hh-dependent tumours and explore its potential as promising target for innovative therapeutic approaches.
Mitochondrial DNA Integrity: Role in Health and Disease
Authors: Sharma Priyanka , Sampath Harini
Published: January 2019

As the primary cellular location for respiration and energy production, mitochondria serve in a critical capacity to the cell. Yet, by virtue of this very function of respiration, mitochondria are subject to constant oxidative stress that can damage one of the unique features of this organelle, its distinct genome. Damage to mitochondrial DNA (mtDNA) and loss of mitochondrial genome integrity is increasingly understood to play a role in the development of both severe early-onset maladies and chronic age-related diseases. In this article, we review the processes by which mtDNA integrity is maintained, with an emphasis on the repair of oxidative DNA lesions, and the cellular consequences of diminished mitochondrial genome stability.
Influence of Green Spaces on Outdoors Thermal Comfort—Structured Experiment in a Mediterranean Climate
Authors: Gonçalves Artur , Castro Ribeiro António , Maia Filipe , Nunes Luís , Feliciano Manuel
Published: January 2019

As a growing part of the global population lives in cities, green spaces are an essential asset for improving quality of life. This study aims to address the role of green spaces in providing favorable thermal comfort conditions for the use of outdoor spaces. The research methodology consisted of a structured experiment where a defined set of individuals from different age groups was exposed to differentiated microclimate conditions. Four nearby locations were considered, ranging from a stone-paved surface without shade to high tree canopy coverage over grass. This experiment took place in three different days in summer and early autumn conditions, with a total of 432 questionnaires. Results show a wide range of thermal sensations found during this experiment, while more favorable thermal sensations were found in shaded locations. To investigate the role of prevailing meteorological and personal conditions on thermal sensations, multinomial logistic regression analysis was applied. Results show the influence of air temperature, global radiation, wind speed, and interviewees’ gender. As meteorological variables were influenced by the diverse contexts found within a close distance inside the studied green space, results from this structured experiment suggest the need for micrometeorological diversity in the local context as a means to promote greater adaptive opportunities for green spaces users.
High Variation in Resource Allocation Strategies among 11 Indian Wheat (Triticum aestivum) Cultivars Growing in High Ozone Environment
Authors: Pandey Ashutosh K. , Majumder Baisakhi , Keski-Saari Sarita , Kontunen-Soppela Sari , Pandey Vivek , Oksanen Elina
Published: January 2019

Eleven local cultivars of wheat (Triticum aestivum) were chosen to study the effect of ambient ozone (O3) concentration in the Indo-Gangetic Plains (IGP) of India at two high-ozone experimental sites by using 300 ppm of Ethylenediurea (EDU) as a chemical protectant against O3. The O3 level was more than double the critical threshold reported for wheat grain production (AOT40 8.66 ppm h). EDU-grown plants had higher grain yield, biomass, stomatal conductance and photosynthesis, less lipid peroxidation, changes in superoxide dismutase and catalase activities, changes in content of oxidized and reduced glutathione compared to non-EDU plants, thus indicating the severity of O3 induced productivity loss. Based on the yield at two different growing sites, the cultivars could be addressed in four response groups: (a) generally well-adapted cultivars (above-average yield); (b) poorly-adapted (below-average yield); (c) adapted to low-yield environment (below-average yield); and (d) sensitive cultivars (adapted to high-yield environment). EDU responses were dependent on the cultivar, the developmental phase (vegetative, flowering and harvest) and the experimental site.
Mechanical and Electroconductive Properties of Mono- and Bilayer Graphene–Carbon Nanotube Films
Authors: Slepchenkov Michael M. , Glukhova Olga E.
Published: January 2019

This article presents the results of a computer study of electrical conductivity and deformation behavior of new graphene–carbon nanotube (CNT) composite films under bending and stretching. Mono- and bilayer hybrid structures with CNTs (10,0) and (12,0) and an inter-tube distance of 10 and 12 hexagons were considered. It is revealed that elastic deformation is characteristic for mono- and bilayer composite films both in bending and stretching. It is found that, in the case of bending in a direction perpendicular to CNTs, the composite film takes the form of an arc, and, in the case of bending in a direction along CNTs, the composite film exhibits behavior that is characteristic of a beam subjected to bending deformation as a result of exposure to vertical force at its free end. It is shown that mono- and bilayer composite films are more resistant to axial stretching in the direction perpendicular to CNTs. The bilayer composite films with an inter-tube distance of 12 hexagons demonstrate the greatest resistance to stretching in a direction perpendicular to CNTs. It is established that the CNT diameter and the inter-tube distance significantly affect the strength limits of composite films under axial stretching in a direction along CNTs. The composite films with CNT (10,0) and an inter-tube distance of 12 hexagons exhibit the highest resistance to stretching in a direction along CNTs. The calculated distribution of local stresses of the atomic network of deformed mono- and bilayer composite films showed that the maximum stresses fall on atoms forming covalent bonds between graphene and CNT, regardless of the CNT diameter and inter-tube distance. The destruction of covalent bonds occurs at the stress of ~1.8 GPa. It is revealed that the electrical resistance of mono- and bilayer composite films decreases with increasing bending. At the same time, the electrical resistance of a bilayer film is 1.5–2 times less than that of a monolayer film. The lowest electrical resistance is observed for composite films with a CNT (12,0) of metallic conductivity.
Effect of Different Polyalcohols as Plasticizers on the Functional Properties of Squid Protein Film (Dosidicus Gigas)
Authors: Murrieta-Martínez Claudia , Soto-Valdez Herlinda , Pacheco-Aguilar Ramón , Torres-Arreola Wilfrido , Rodríguez-Felix Francisco , Ramírez-Wong Benjamín , Santacruz-Ortega Hisila , Santos-Sauceda Irela , Olibarría-Rodríguez Guillermo , Márquez-Ríos Enrique
Published: January 2019

Conventional plastic materials accumulation has led to a constant search to develop friendly packaging, edible coatings from biopolymers are an example. Since different proteins have different behavior and plastizicer compatibility, in this work, the effect of different polyalcohols (glycerol, sorbitol, maltitol, mannitol, and xylitol) as plasticizers on squid protein films behavior was studied. The results show that except for mannitol, transparent, and flexible films can be obtained. None of them showed transmission to light on the ultraviolet (UV) spectrum. However, only glycerol and sorbitol were sufficiently flexible to evaluate their mechanical properties, in which glycerol had a more elastic behavior with an elongation at a break of 920% and tensile strength (TS) of 0.94 MPa, while sorbitol exhibited a more plastic behavior with an elongation at break of 511% and a TS of 4.41 MPa. Water-vapor transmission rate was higher in glycerol, with 194.41 g·m−2d−1, while sorbitol had 44.27 g·m−2d−1 but presented blooming. This could be due to low interaction between sorbitol and the protein matrix, correlating with the film-solubility results. Amide I band of the Fourier transform infrared (FT-IR) spectra demonstrated higher denaturation and loss of alpha helical structure in glycerol film, followed by maltitol/sorbitol, xylitol, mannitol, and the control film. This in accordance with thermogravimetric analysis (TGA) results. The results of this study prove that only glycerol and sorbitol are suitable to obtain a see-through flexible film.