bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal development of the oral microbiome and prediction of early childhood caries
Authors: Dashper S. G. , Mitchell H. L. , Lê Cao K.-A. , Carpenter L. , Gussy M. G. , Calache H. , Gladman S. L. , Bulach D. M. , Hoffmann B. , Catmull D. V. , Pruilh S. , Johnson S. , Gibbs L. , Amezdroz E. , Bhatnagar U. , Seemann T. , Mnatzaganian G. , Manton D. J. , Reynolds E. C. 
Published: December 2019

AbstractHuman microbiomes are predicted to assemble in a reproducible and ordered manner yet there is limited knowledge on the development of the complex bacterial communities that constitute the oral microbiome. The oral microbiome plays major roles in many oral diseases including early childhood caries (ECC), which afflicts up to 70% of children in some countries. Saliva contains oral bacteria that are indicative of the whole oral microbiome and may have the ability to reflect the dysbiosis in supragingival plaque communities that initiates the clinical manifestations of ECC. The aim of this study was to determine the assembly of the oral microbiome during the first four years of life and compare it with the clinical development of ECC. The oral microbiomes of 134 children enrolled in a birth cohort study were determined at six ages between two months and four years-of-age and their mother’s oral microbiome was determined at a single time point. We identified and quantified 356 operational taxonomic units (OTUs) of bacteria in saliva by sequencing the V4 region of the bacterial 16S RNA genes. Bacterial alpha diversity increased from a mean of 31 OTUs in the saliva of infants at 1.9 months-of-age to 84 OTUs at 39 months-of-age. The oral microbiome showed a distinct shift in composition as the children matured. The microbiome data were compared with the clinical development of ECC in the cohort at 39, 48, and 60 months-of-age as determined by ICDAS-II assessment. Streptococcus mutans was the most discriminatory oral bacterial species between health and current disease, with an increased abundance in disease. Overall our study demonstrates an ordered temporal development of the oral microbiome, describes a limited core oral microbiome and indicates that saliva testing of infants may help predict ECC risk.
Raman spectroscopy as a non-invasive diagnostic technique for endometriosis
Authors: Parlatan Ugur , Inanc Medine Tuna , Ozgor Bahar Yuksel , Oral Engin , Bastu Ercan , Unlu Mehmet Burcin , Basar Gunay 
Published: December 2019

AbstractEndometriosis is a condition in which the endometrium, the layer of tissue that usually covers the inside of the uterus, grows outside the uterus. One of its severe effects is sub-fertility. The exact reason for endometriosis is still unknown and under investigation. Tracking the symptoms is not sufficient for diagnosing the disease. A successful diagnosis can only be made using laparoscopy. During the disease, the amount of some molecules (i.e., proteins, antigens) changes in the blood. Raman spectroscopy provides information about biochemicals without using dyes or external labels. In this study, Raman spectroscopy is used as a non-invasive diagnostic method for endometriosis. The Raman spectra of 94 serum samples acquired from 49 patients and 45 healthy individuals were compared for this study. Principal Component Analysis (PCA), k- Nearest Neighbors (kNN), and Support Vector Machines (SVM) were used in the analysis. According to the results (using 80 measurements for training and 14 measurements for the test set), it was found that kNN-weighted gave the best classification model with sensitivity and specificity values of 80.5% and 89.7%, respectively. Testing the model with unseen data yielded a sensitivity value of 100% and a specificity value of 100%. To the best of our knowledge, this is the first study in which Raman spectroscopy was used in combination with PCA and classification algorithms as a non-invasive method applied on blood sera for the diagnosis of endometriosis.
Vitamin C and aroma composition of fresh leaves from Kalanchoe pinnata and Kalanchoe daigremontiana
Authors: Zawirska-Wojtasiak Renata , Jankowska Beata , Piechowska Paulina , Mildner-Szkudlarz Sylwia 
Published: December 2019

AbstractSpecies of kalanchoe are rich in bioactive compounds and are widely used in folk medicine; however, these plants are not well known from the point of view of aroma. Two species, Kalanchoe pinnata and Kalanchoe daigremontiana, were examined after six months and two years of growth and their vitamin C content, succulence, and aroma composition were determined. The efficiency of juice extraction was highest (72%) for the leaves of K. daigremontiana after six months of growth. The concentration of vitamin C was highest in juices from two-year-old plants and much higher in the juice of K. pinnata (81 mg/100 g). SPME/GC/MS analysis identified 32 aroma components, considering those with the spectrum similarity over 75%. The main components were furan-2-ethyl, hexanal, 2-hexenal, 2,4-hexadienal, 1-octen-3-ol, nonanal. The quantitative relations of these compounds were somewhat different in the two species. The most dominant component, 2-hexenal, is responsible for the green-like aroma noted by the sensory panel.
Circular METRN RNA hsa_circ_0037251 Promotes Glioma Progression by Sponging miR-1229-3p and Regulating mTOR Expression
Authors: Cao Qinchen , Shi Yonggang , Wang Xinxin , Yang Jing , Mi Yin , Zhai Guan , Zhang Mingzhi 
Published: December 2019

AbstractCircular RNAs (circRNAs) are a newly identifed non-coding RNA in many cellular processes and tumours. This study aimed to investigate the role of hsa_circ_0037251, one circRNA generated from several exons of the gene termed METRN, in glioma progression. Through in vitro experiments, we discovered that high expression of hsa_circ_0037251 was related to low expression of the microRNA miR-1229-3p and high expression of mTOR. The over-expressed hsa_circ_0037251 promoted cell proliferation, invasion and migration in glioma, while knockdown of hsa_circ_00037251 promoted cell apoptosis and induced G1 phase arrest. Then, hsa_circ_0037251 was observed to directly sponge miR-1229-3p, and mTOR was identified as a direct target of miR-1229-3p. In addition, knockdown of hsa_circ_0037251 up-regulated the expression of miR-1229-3p and inhibited the expression of mTOR. And overexpression of miR-1229-3p or low-expressed mTOR inhibited the glioma cell progression. Furthermore, transfection with mTOR overexpression vectors can restore the abilities of glioma cell progression even if hsa_circ_00037251 was knocked down using siRNAs. In vivo experiments revealed that hsa_circ_00037251 promoted the growth of xenografted tumours and shortened the survival period. These results indicated that hsa_circ_0037251 may act as a tumour promoter by a hsa_circ_0037251/miR-1229-3p/mTOR axis, and these potential biomarkers may be therapeutic targets for glioma.
Prefrontal parvalbumin cells are sensitive to stress and mediate anxiety-related behaviors in female mice
Authors: Page Chloe E. , Shepard Ryan , Heslin Kelsey , Coutellier Laurence 
Published: December 2019

AbstractReduced activity of the prefrontal cortex (PFC) is seen in mood disorders including depression and anxiety. The mechanisms of this hypofrontality remain unclear. Because of their specific physiological properties, parvalbumin-expressing (PV+) inhibitory interneurons contribute to the overall activity of the PFC. Our recent work using a chronic stress mouse model showed that stress-induced increases in prefrontal PV expression correlates with increased anxiety-like behaviors in female mice. Our goal is now to provide a causal relationship between changes in prefrontal PV+ cells and changes in emotional behaviors in mice. We first show that, in addition to increasing overall level of PV expression, chronic stress increases the activity of prefrontal PV+ cells. We then used a chemogenetic approach to mimic the effects of chronic stress and specifically increase the activity of prefrontal PV+ cells. We observed that chemogenetic activation of PV+ cells caused an overall reduction in prefrontal activity, and that chronic activation of PV+ cells lead to increased anxiety-related behaviors in female mice only. These results demonstrate that activity of prefrontal PV+ cells could represent a novel sex-specific modulator of anxiety-related behaviors, potentially through changes in overall prefrontal activity. The findings also support the idea that prefrontal PV+ cells are worth further investigation to better understand mood disorders that are more prevalent in female populations.
A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains
Authors: Modi Vivek , Dunbrack Roland L. 
Published: December 2019

AbstractStudies on the structures and functions of individual kinases have been used to understand the biological properties of other kinases that do not yet have experimental structures. The key factor in accurate inference by homology is an accurate sequence alignment. We present a parsimonious, structure-based multiple sequence alignment (MSA) of 497 human protein kinase domains excluding atypical kinases. The alignment is arranged in 17 blocks of conserved regions and unaligned blocks in between that contain insertions of varying lengths present in only a subset of kinases. The aligned blocks contain well-conserved elements of secondary structure and well-known functional motifs, such as the DFG and HRD motifs. From pairwise, all-against-all alignment of 272 human kinase structures, we estimate the accuracy of our MSA to be 97%. The remaining inaccuracy comes from a few structures with shifted elements of secondary structure, and from the boundaries of aligned and unaligned regions, where compromises need to be made to encompass the majority of kinases. A new phylogeny of the protein kinase domains in the human genome based on our alignment indicates that ten kinases previously labeled as “OTHER” can be confidently placed into the CAMK group. These kinases comprise the Aurora kinases, Polo kinases, and calcium/calmodulin-dependent kinase kinases.
RETRACTED: Characterising the spatial and temporal brain metal profile in a mouse model of tauopathy
Authors: Rao Shalini S , Lago Larissa , Gonzalez de Vega Raquel , Bray Lisa , Hare Dominic J , Clases David , Doble Philip A , Adlard Paul A 
Published: December 2019

Abstract
A dysregulation in the homeostasis of metals such as copper, iron and zinc is speculated to be involved in the pathogenesis of tauopathies, which includes Alzheimer's disease (AD). In particular, there is a growing body of evidence to support a role for iron in facilitating the hyperphosphorylation and aggregation of the tau protein into neurofibrillary tangles (NFTs) – a primary neuropathological hallmark of tauopathies. Therefore, the aim of this study was to characterize the spatial and temporal brain metallomic profile in a mouse model of tauopathy (rTg(tauP301L)4510), so as to provide some insight into the potential interaction between tau pathology and iron. Using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), our results revealed an age-dependent increase in brain iron levels in both WT and rTg(tauP301L)4510 mice. In addition, size exclusion chromatography-ICP-MS (SEC-ICP-MS) revealed significant age-related changes in iron bound to metalloproteins such as ferritin. The outcomes from this study may provide valuable insight into the inter-relationship between iron and tau in ageing and neurodegeneration.
Hypochlorous acid-mediated modification of proteins and its consequences
Authors: Hawkins Clare L. 
Published: December 2019

Abstract
Myeloperoxidase (MPO) is a mammalian heme peroxidase released by activated immune cells, which forms chemical oxidants, including hypochlorous acid (HOCl), to kill bacteria and other invading pathogens. In addition to this important role in the innate immune system, there is significant evidence from numerous chronic inflammatory pathologies for the elevated production of HOCl and associated oxidative modification of proteins and damage to host tissue. Proteins are major targets for HOCl in biological systems, owing to their abundance and the high reactivity of several amino acid side-chains with this oxidant. As such, there is significant interest in understanding the molecular mechanisms involved in HOCl-mediated protein damage and defining the consequences of these reactions. Exposure of proteins to HOCl results in a wide range of oxidative modifications and the formation of chlorinated products, which alter protein structure and enzyme activity, and impact the function of biological systems. This review describes the reactivity of HOCl with proteins, including the specific pathways involved in side-chain modification, backbone fragmentation and aggregation, and outlines examples of some of the biological consequences of these reactions, particularly in relation to the development of chronic inflammatory disease.
How It Works in the Real World: Helping Students Navigate Clinical Placements
Authors: Bice Ed M. , Smith Pamela A. 
Published: December 2019

Purpose
This article discusses current issues found in external clinical placements and their possible causes, and this offers practical solutions for assisting students to benefit from their experiences. In order to obtain a Certificate of Clinical Competence from the American Speech-Language-Hearing Association, students must obtain a required number of patient contact hours. Many of these experiences are supervised by a mentor outside of the university setting. This provides opportunity for the student to be exposed to various clinical philosophies. It also opens the possibility that the student will be exposed to practices that are not based in sound theory or evidence.

Conclusion
Preparing students to assess and manage clinical placements is vital to their success. Several suggestions for encouraging and facilitating productive clinical conversations between mentor and mentee are proposed.
PDMS‐based hot embossing method of fabricating SU‐8 photoresist conical nozzle for inkjet print‐head
Authors: Yan Shixia , Wang Xing , Li Kehong , Wang Fengwei , Guo Ran , Zou Helin 
Published: December 2019

This work reports a PDMS‐based hot embossing technique. The proposed method enables rapid, low‐cost and mass‐produced fabrication of SU‐8 photoresist conical nozzle for inkjet print‐head with soft PDMS moulds. The hydrophobic time for SU‐8 master mould treated by trimethyldichlorosilane (TMCS) was determined. And the optimised thickness of SU‐8 photoresist before hot embossing was 58.5 ± 1.55 μm corresponding to 3750 r/min of spin coating speed. The imprinting parameters were investigated. The highest replication precision was obtained in the embossed SU‐8 conical nozzle processed by an embossing pressure of 2.57 MPa, an embossing temperature of 80°C, and an embossing time of 6 min. Finally, this work presents the fabrication of the SU‐8 conical nozzle plate with the large aperture of 40.01 ± 1.24 μm, small aperture of 27.12 ± 1.07 μm, and the nozzle height of 50 ± 1.26 μm.
How planets grow by pebble accretion
Authors: Brouwers M. G. , Ormel C. W. 
Published: December 2019

Context. Proto-planets embedded in their natal disks acquire hot envelopes as they grow and accrete solids. This ensures that the material they accrete – pebbles, as well as (small) planetesimals – will vaporize to enrich their atmospheres. Enrichment modifies an envelope’s structure and significantly alters its further evolution.
Aims. Our aim is to describe the formation of planets with polluted envelopes from the moment that impactors begin to sublimate to beyond the disk’s eventual dissipation.
Methods. We constructed an analytical interior structure model, characterized by a hot and uniformly mixed high-Z vapor layer surrounding the core, located below the usual unpolluted radiative-convective regions. Our model assumes an ideal equation of state and focuses on identifying trends rather than precise calculations. The expressions we derived are applicable to all single-species pollutants, but we used SiO2 to visualize our results.
Results. The evolution of planets with uniformly mixed polluted envelopes follows four potential phases. Initially, the central core grows directly through impacts and rainout until the envelope becomes hot enough to vaporize and absorb all incoming solids. We find that a planet reaches runaway accretion when the sum of its core and vapor mass exceeds a value that we refer to as the critical metal mass – a criterion that supersedes the traditional critical core mass. The critical metal mass scales positively with both the pollutant’s evaporation temperature and with the planet’s core mass. Hence, planets at shorter orbital separations require the accretion of more solids to reach runaway as they accrete less volatile materials. If the solids accretion rate dries up, we identify the decline of the mean molecular weight – dilution – as a mechanism to limit gas accretion during a polluted planet’s embedded cooling phase. When the disk ultimately dissipates, the envelope’s inner temperature declines and its vapor eventually rains out, augmenting the mass of the core. The energy release that accompanies this does not result in significant mass-loss, as it only occurs after the planet has substantially contracted.
Should We Make More Bone or Not, As Told by Kisspeptin Neurons in the Arcuate Nucleus
Authors: Herber Candice B. , Ingraham Holly A. 
Published: December 2019

AbstractSince its initial discovery in 2002, the neuropeptide Kisspeptin (Kiss1) has been anointed as the master regulator controlling the onset of puberty in males and females. Over the last several years, multiple groups found that Kiss1 signaling is mediated by the 7TM surface receptor GPCR54. Kiss1 mRNA is highly enriched in the basal medial and lateral subregions of the arcuate nucleus (ARC) in the medial basal hypothalamus. Thus, Kiss1ARC neurons reside in a unique anatomical location ideal for sensing and responding to circulating steroid hormones as well as nutrients. Kiss1 expression is highly responsive to fluctuations of the gonadal hormone, estrogen, with nearly 90% of Kiss1ARC neurons expressing the nuclear hormone estrogen receptor alpha (ERa). Here we review recent research that extends the function of Kiss1ARC neurons beyond the regulation of puberty and highlight their emerging, novel roles in controlling energy allocation, behavioral outputs, and sex-dependent bone remodeling in females. Indeed, some of these previously unknown functions for Kiss1 neurons are quite striking as exemplified by the remarkable increase in bone mass after manipulating estrogen signaling in Kiss1ARC neurons. Taken together, we suggest that Kiss1ARC neurons are highly sensitive to nutritional and hormonal cues that dictate energy utilization and reproduction.
Ellagitannins from Punica granatum leaves suppress microsomal prostaglandin E synthase-1 expression and induce lung cancer cells to undergo apoptosis
Authors: Toda Keisuke , Ueyama Mai , Tanaka Shomu , Tsukayama Izumi , Mega Takuto , Konoike Yuka , Tamenobu Asako , Bastian Februadi , Akai Iria , Ito Hideyuki , Kawakami Yuki , Takahashi Yoshitaka , Suzuki-Yamamoto Toshiko 
Published: December 2019

ABSTRACT
Prostaglandin E2 (PGE2), which is a potent pro-inflammatory lipid mediator, is biosynthesized from arachidonic acid by cyclooxygenase-2 (COX-2) and microsomal PGE synthase-1 (mPGES-1). Non-steroidal anti-inflammatory drugs (NSAIDs) are used clinically as COX inhibitors, but they have gastrointestinal and cardiovascular side-effects. Thus, the terminal enzyme mPGES-1 holds promise as the next therapeutic target. In this study, we found that the ellagitannins granatin A and granatin B isolated from pomegranate leaves, and geraniin, which is their structural analog, selectively suppressed mPGES-1 expression without affecting COX-2 in non-small cell lung carcinoma A549 cells. The ellagitannins also down-regulated tumor necrosis factor α, inducible nitric oxide synthase, and anti-apoptotic factor B-cell chronic lymphocytic leukemia/lymphoma 2, and induced A549 cells to undergo apoptosis. These findings indicate that the ellagitannins have anti-inflammatory and anti-carcinogenic effects, due to their specific suppression of mPGES-1.
Abbreviations: Bcl-2: B-cell chronic lymphocytic leukemia/lymphoma 2; COX: cyclooxygenase; CRE: cAMP response element; DHHDP: dehydrohexahydroxydiphenoyl; Et2O: diethyl ether; EtOAc: ethyl acetate; GAPDH: glyceraldehyde 3-phosphate dehydrogenase; iNOS: inducible nitric oxide synthase; mPGES-1: microsomal prostaglandin E synthase-1; n-BuOH: water-saturated n-butanol; NSAIDs: non-steroidal anti-inflammatory drugs; NF-κB: nuclear factor-κB; PG: prostaglandin; TNF: tumor necrosis factor; TUNEL: terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling
Water quality simulation for rehabilitation of a eutrophic lake in Selangor, Malaysia
Authors: Koh H L , Tan W K , Teh S Y , Tay C J 
Published: December 2019

Abstract
More than 50 % of lakes worldwide, including 60 % in Malaysia, are contaminated by eutrophication due to excessive nutrient inputs. These nutrients include phosphorus and nitrogen derived from agriculture, industry and domestic wastes. Eutrophication is an undesirable lake condition characterized by turbid water and dominated by abundant growth of algae, resulting in suppressed macrophytes and in reduced ecosystem services. Healthy lakes provide ecosystem services that have been valued to be worth billions to the Malaysian Gross Domestic Production annually. Rehabilitation of eutrophic lakes located in urban areas is therefore urgently needed. A recreational lake located in Selangor Malaysia has shown persistent signs of eutrophication with chlorophyll-a level fluctuating between 10 and 25 µg/L. Left untreated, the lake water quality will deteriorate further, potentially inducing a regime shift to hypereutrophic condition, caused by intense interaction between water column phosphorus and sediment phosphorus. Based upon water and sediment quality data compiled over the last eight years, this paper presents analysis and model simulations for implementation of a sustainable program for controlling eutrophication using low cost technology.
Assessing phytoplankton distribution and water quality in constructed wetlands during dry and wet periods: A Case Study in USM Engineering Campus
Authors: Shaharuddin S , Zakaria NA , Ghani Ab , Wan Maznah WO 
Published: December 2019

Abstract
Constructed wetlands (CW) are built to improve water quality while serving as an alternative sustainable habitat for aquatic life. In Malaysia, CWs are designed according to the guideline for Urban Stormwater Management Manual for Malaysia (MSMA 2nd Edition) 2012. This study shall evaluate the performance of constructed wetland design as stipulated by MSMA through assessment of water quality and phytoplankton growth, which acts as a biodiversity indicator. A 5-month sampling period with phytoplankton abundance in a constructed wetland was correlated with the selected water quality index (WQI) parameters comprising dissolved oxygen (DO), ammoniacal oxygen (AN), chemical oxygen demand (COD), biological oxygen demand (BOD), total suspended solid (TSS), and pH. The constructed wetland consists of three main zones, namely the forebay, macrophytes and micropool zones. The highest WQI value was obtained from the micropool zone with a range of 78.98-85.45 (82.71±3.35) while the lowest WQI value was collected from the macrophytes zone with a range of 68.13-77.96 (73.25±3.42). A total of 15 phytoplankton species from 5 different algal phyla were identified in the constructed wetland. Phytoplankton distribution was high in the macrophytes zone (521 cell m-3) during dry season due to high nutrient concentration as opposed to the other zones. The phytoplankton distribution was found to be closely associated with DO, AN, TSS and total phosphorus. At the same time, the macrophyte zone design also affects the distribution of phytoplankton.