bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and control for the effects of bioinformatic globin depletion on human RNA-seq differential expression analysis
Authors: Sheerin Dylan , Lakay Francisco , Esmail Hanif , Kinnear Craig , Sansom Bianca , Glanzmann Brigitte , Wilkinson Robert J. , Ritchie Matthew E. , Coussens Anna K. 
Published: February 2023

AbstractWhen profiling blood samples by RNA-sequencing (RNA-seq), RNA from haemoglobin (Hgb) can account for up to 70% of the transcriptome. Due to considerations of sequencing depth and power to detect biological variation, Hgb RNA is typically depleted prior to sequencing by hybridisation-based methods; an alternative approach is to deplete reads arising from Hgb RNA bioinformatically. In the present study, we compared the impact of these two approaches on the outcome of differential gene expression analysis performed using RNA-seq data from 58 human tuberculosis (TB) patient or contact whole blood samples–29 globin kit-depleted and 29 matched non-depleted—a subset of which were taken at TB diagnosis and at six months post-TB treatment from the same patient. Bioinformatic depletion of Hgb genes from the non-depleted samples (bioinformatic-depleted) substantially reduced library sizes (median = 57.24%) and fewer long non-coding, micro, small nuclear and small nucleolar RNAs were captured in these libraries. Profiling published TB gene signatures across all samples revealed inferior correlation between kit-depleted and bioinformatic-depleted pairs when the proportion of reads mapping to Hgb genes was higher in the non-depleted sample, particularly at the TB diagnosis time point. A set of putative “globin-fingerprint” genes were identified by directly comparing kit-depleted and bioinformatic-depleted samples at each timepoint. Two TB treatment response signatures were also shown to have decreased differential performance when comparing samples at TB diagnosis to six months post-TB treatment when profiled on the bioinformatic-depleted samples compared with their kit-depleted counterparts. These results demonstrate that failure to deplete Hgb RNA prior to sequencing has a negative impact on the sensitivity to detect disease-relevant gene expression changes even when bioinformatic removal is performed.
Endoplasmic reticulum stress inhibition ameliorated WFS1 expression alterations and reduced pancreatic islets’ insulin secretion induced by high-fat diet in rats
Authors: Binayi Fateme , Fahanik-Babaei Javad , Salimi Mina , Eskandari Farzaneh , Sahraei Mohammad , Ghorbani Ranjbary Ali , Ghasemi Rasoul , Hedayati Mehdi , Khodagholi Fariba , Eliassi Afsaneh , Zardooz Homeira 
Published: February 2023

AbstractEndoplasmic reticulum (ER) stress is involved in the development of glucose homeostasis impairment. When ER stress occurs, the unfolded protein response (UPR) is activated to cope with it. One of the UPR components is WFS1 (Wolfram syndrome 1), which plays important roles in ER homeostasis and pancreatic islets glucose-stimulated insulin secretion (GSIS). Accordingly and considering that feeding high-fat food has a major contribution in metabolic disorders, this study aimed to investigate the possible involvement of pancreatic ER stress in glucose metabolism impairment induced by feeding high-fat diet (HFD) in male rats. After weaning, the rats were divided into six groups, and fed on normal diet and HFD for 20 weeks, then 4-phenyl butyric acid (4-PBA, an ER stress inhibitor) was administered. Subsequently, in all groups, after performing glucose tolerance test, the animals were dissected and their pancreases were removed to extract ER, islets isolation and assessment of GSIS. Moreover, the pancreatic ER stress [binding of immunoglobulin protein (BIP) and enhancer-binding protein homologous protein (CHOP)] and oxidative stress [malondialdehyde (MDA), glutathione (GSH) and catalase] biomarkers as well as WFS1 expression level were evaluated. HFD decreased pancreatic WFS1 protein and GSH levels, and enhanced pancreatic catalase activity, MDA content, BIP and CHOP protein and mRNA levels as well as Wfs1 mRNA amount. Accordingly, it increased BIP, CHOP and WFS1 protein levels in the extracted ER of pancreas. In addition, the HFD caused glucose intolerance, and decreased the islets’ GSIS and insulin content. However, 4-PBA administration restored the alterations. It seems that, HFD consumption through inducing pancreatic ER stress, altered WFS1 expression levels, reduced the islets’ GSIS and insulin content and finally impaired glucose homeostasis.
Diagnostic accuracy of the Enferplex Bovine Tuberculosis antibody test in cattle sera
Authors: O’Brien Amanda , Clarke John , Hayton Alastair , Adler Andy , Cutler Keith , Shaw Darren J. , Whelan Clare , Watt Neil J. , Harkiss Gordon D. 
Published: February 2023

AbstractBovine tuberculosis is a contagious bacterial disease of worldwide economic, zoonotic and welfare importance caused mainly by Mycobacterium bovis infection. Current regulatory diagnostic methods lack sensitivity and require improvement. We have developed a multiplex serological test for bovine tuberculosis and here we provide an estimate of the diagnostic accuracy of the test in cattle. Positive and negative reference serum samples were obtained from animals from Europe and the United States of America. The diagnostic specificity estimate was 98.4% and 99.7% using high sensitivity and high specificity settings of the test respectively. Tuberculin boosting did not affect the overall specificity estimate. The diagnostic sensitivity in samples from Mycobacterium bovis culture positive animals following tuberculin boosting was 93.9%.The relative sensitivity following boosting in tuberculin test positive, lesion positive animals and interferon gamma test positive, lesion positive animals was 97.2% and 96.9% respectively. In tuberculin test negative, lesion positive animals and in interferon gamma test negative, lesion positive animals, the relative sensitivity following tuberculin boosting was 88.2% and 83.6% respectively. The results show that the test has high diagnostic sensitivity and specificity and can detect infected animals that are missed by tuberculin and interferon gamma testing.
Investigation on the site of coronal deformities in Hallux valgus
Authors: Wei Rachel Xiaoyu , Ko Violet Man-chi , Chui Elvis Chun-sing , Fu Bruma Sai-chuen , Hung Vivian Wing-yin , Yung Patrick Shu-hang , Ling Samuel Ka-kin 
Published: February 2023

AbstractHallux valgus (HV) is a common foot deformity that is more prevalent in females, characterised by abnormal adduction of the first metatarsal (MT) and valgus deviation of the phalanx on the transverse plane. Increasing evidence indicates that HV is more than a 2D deformity but a 3D one with rotational malalignment. Pronation deformity is seen during clinical examination for HV patients, but the exact origin of this rotational deformity is still unknown. Some attribute it to first tarsometatarsal (TMT) joint rotation, while others attribute it to intra-metatarsal bony torsion. In addition, the correlation between the rotational and transverse plane deformity is inconclusive. Identifying the origin of the rotational deformity will help surgeons choose the optimal surgical procedure while also enhancing our understanding of the pathophysiology of HV. This study aims to (1) develop an objective method for measuring the first MT torsion and first TMT joint rotation; (2) investigate the exact location of the coronal deformity in HV; (3) investigate the relationship between the severity of deformity on the transverse and coronal planes as well as the correlation between deformity severity and foot function/symptoms in HV. Age-matched females with and without HV were recruited at the Foot and Ankle Clinic of the Department of Orthopaedics and Traumatology. Computed tomography was conducted for all subjects with additional weight-bearing dorsal-plantar X-ray examination for HV subjects. Demographic information of all subjects was recorded, with symptoms and functions related to HV evaluated. The intra-class correlation was used to explore the relationship between deformities on different planes and the deformity severity and functional outcomes, respectively. An Independent t-test was used to compare joint rotation and bone torsion degrees. TMT joint rotation is significantly correlated with foot function. HV patients had more TMT joint rotation but not MT torsion compared to normal controls. No relationship was found between the coronal rotation and the 1,2-intermetatarsal angle (IMA) or Hallux valgus angle (HVA) on the transverse plane. Our results indicate that coronal deformities in HV may originate from TMT joint rotation. In addition, the severity of the TMT joint coronal rotation correlates with worse foot function; thus, multi-plane assessment and examination will be necessary for more precise surgical correction.
Oxygenated hemoglobin as prognostic marker among patients with systemic sclerosis screened for pulmonary hypertension
Authors: Xanthouli Panagiota , Gordjani Ojan , Benjamin Nicola , Trudzinski Franziska C. , Egenlauf Benjamin , Harutyunova Satenik , Marra Alberto M. , Milde Nicklas , Nagel Christian , Blank Norbert , Lorenz Hanns-Martin , Grünig Ekkehard , Eichstaedt Christina A. 
Published: February 2023

AbstractOxygenated hemoglobin (OxyHem) in arterial blood may reflect disease severity in patients with systemic sclerosis (SSc). The aim of this study was to analyze the predictive value of OxyHem in SSc patients screened for pulmonary hypertension (PH). OxyHem (g/dl) was measured by multiplying the concentration of hemoglobin with fractional oxygen saturation in arterialized capillary blood. Prognostic power was compared with known prognostic parameters in SSc using uni- and multivariable analysis. A total of 280 SSc patients were screened, 267 were included in the analysis. No signs of pulmonary vascular disease were found in 126 patients, while 141 patients presented with mean pulmonary arterial pressure ≥ 21 mmHg. Interstitial lung disease (ILD) was identified in 70 patients. Low OxyHem ≤ 12.5 g/dl at baseline was significantly associated with worse survival (P = 0.046). In the multivariable analysis presence of ILD, age ≥ 60 years and diffusion capacity for carbon monoxide (DLCO) ≤ 65% were negatively associated with survival. The combination of low DLCO and low OxyHem at baseline could predict PH at baseline (sensitivity 76.1%). This study detected for the first time OxyHem ≤ 12.5 g/dl as a prognostic predictor in SSc patients. Further studies are needed to confirm these results.
The graph structure of two-player games
Authors: Biggar Oliver , Shames Iman 
Published: February 2023

AbstractIn this paper, we analyse two-player games by their response graphs. The response graph has nodes which are strategy profiles, with an arc between profiles if they differ in the strategy of a single player, with the direction of the arc indicating the preferred option for that player. Response graphs, and particularly their sink strongly connected components, play an important role in modern techniques in evolutionary game theory and multi-agent learning. We show that the response graph is a simple and well-motivated model of strategic interaction which captures many non-trivial properties of a game, despite not depending on cardinal payoffs. We characterise the games which share a response graph with a zero-sum or potential game respectively, and demonstrate a duality between these sets. This allows us to understand the influence of these properties on the response graph. The response graphs of Matching Pennies and Coordination are shown to play a key role in all two-player games: every non-iteratively-dominated strategy takes part in a subgame with these graph structures. As a corollary, any game sharing a response graph with both a zero-sum game and potential game must be dominance-solvable. Finally, we demonstrate our results on some larger games.
Simultaneous determination of volatile phenol, cyanide, anionic surfactant, and ammonia nitrogen in drinking water by a continuous flow analyzer
Authors: Qin Guofu , Zou Keting , He Fengrui , Shao Ji , Zuo Bei , Liu Jia , Liu Ruixiao , Yang Bixia , Zhao Guipeng 
Published: February 2023

AbstractThis study developed a method for the simultaneous determination of volatile phenol, cyanide, anionic surfactant, and ammonia nitrogen in drinking water, using a continuous flow analyzer. The samples were first distilled at 145 °C. The phenol in the distillate then subsequently reacted with alkaline ferricyanide and 4-aminoantipyrine to form a red complex that was measured colorimetrically at 505 nm. Cyanide in the distillate subsequently reacted with chloramine T to form cyanogen chloride, which then formed a blue complex with pyridinecarboxylic acid that was measured colorimetrically at 630 nm. The anionic surfactant reacted with basic methylene blue to form a compound that was extracted into chloroform and washed with acidic methylene blue to remove interfering substances. The blue compound in chloroform was determined colorimetrically at 660 nm. Ammonia reacted with salicylate and chlorine from dichloroisocyanuric acid to produce indophenol blue at 37 °C in an alkaline environment that was measured at 660 nm. The relative standard deviations were 0.75–6.10% and 0.36–5.41%, respectively, and the recoveries were 96.2–103.6% and 96.0–102.4% when the mass concentration of volatile phenol and cyanide was in the range of 2–100 μg/L. The linear correlation coefficients were ≥ 0.9999, and the detection limits were1.2 μg/L and 0.9 μg/L, respectively. The relative standard deviations were 0.27–4.86% and 0.33–5.39%, and the recoveries were 93.7–107.0% and 94.4–101.7%. When the mass concentration of anionic surfactant and ammonia nitrogen was 10–1000 μg/L. The linear correlation coefficients were 0.9995 and 0.9999, and the detection limits were 10.7 μg/L and 7.3 μg/L, respectively. When compared to the national standard method, no statistically significant difference was found. This approach saves time and labor, has a lower detection limit, higher precision and accuracy, less contamination, and is more appropriate for the analysis and determination of large-volume samples.
Impact of air pollution on running performance
Authors: Cusick Marika , Rowland Sebastian T. , DeFelice Nicholas 
Published: February 2023

AbstractAir pollution exposures during training may impact race performances. We aggregated data on 334 collegiate male track & field athletes from 46 universities across the United States over 2010–2014. Using distributed lag non-linear models, we analyzed the relationship between race time and PM2.5, ozone, and two versions of the Air Quality Index (AQI) exposures up to 21 days prior to the race. We observed a 12.8 (95% CI: 1.3, 24.2) second and 11.5 (95% CI: 0.8, 22.1) second increase in race times from 21 days of PM2.5 exposure (10.0 versus 5.0 μg/m3) and ozone exposure (54.9 versus 36.9 ppm), respectively. Exposure measured by the two-pollutant threshold (PM2.5 and ozone) AQI was not significantly associated with race time; however, the association for summed two-pollutant AQI (PM2.5 plus ozone) was similar to associations observed for the individual pollutants (12.4, 95% CI: 1.8, 23.0 s). Training and competing at elevated air pollution levels, even at exposures within AQI’s good-to-moderate classifications, was associated with slower race times. This work provides an initial characterization of the effect of air pollution on running performance and a justification for why coaches should consider approaches to reduce air pollution exposures while training.
Majority networks and local consensus algorithm
Authors: Goles Eric , Medina Pablo , Santiváñez Julio 
Published: February 2023

AbstractIn this paper, we study consensus behavior based on the local application of the majority consensus algorithm (a generalization of the majority rule) over four-connected bi-dimensional networks. In this context, we characterize theoretically every four-vicinity network in its capacity to reach consensus (every individual at the same opinion) for any initial configuration of binary opinions. Theoretically, we determine all regular grids with four neighbors in which consensus is reached and in which ones not. In addition, in those instances in which consensus is not reached, we characterize statistically the proportion of configurations that reach spurious fixed points from an ensemble of random initial configurations. Using numerical simulations, we also analyze two observables of the system to characterize the algorithm: (1) the quality of the achieved consensus, that is if it respects the initial majority of the network; and (2) the consensus time, measured as the average amount of steps to reach convergence.
Spider mites avoid caterpillar traces to prevent intraguild predation
Authors: Kinto Shiori , Akino Toshiharu , Yano Shuichi 
Published: February 2023

AbstractThe phytophagous spider mites Tetranychus kanzawai and Tetranychus urticae can be as small as < 0.5 mm; thus, they are often incidentally consumed along with food plant leaves by voracious lepidopteran larvae (hereafter, ‘caterpillars’). Therefore, the ability to avoid such intraguild predation should confer a selective advantage to mites. We experimentally demonstrated that adult females of both mite species avoided settling on food plant leaves with traces of all tested caterpillar species (Bombyx mori, Papilio xuthus, Spodoptera litura and Theretra oldenlandiae). We examined additional interactions using B. mori and T. kanzawai and found that B. mori trace avoidance by T. kanzawai lasted for more than 48 h. Tetranychus kanzawai also avoided B. mori traces on plant stems, along which mites access leaves. Moreover, T. kanzawai avoided acetone extracts of B. mori traces applied to filter paper, indicating that chemical substances of caterpillar traces are responsible for the avoidance. This study is the first demonstration of a repellent effect of herbivore trace chemicals on heterospecific herbivores. Although spider mites have developed resistance against many synthetic pesticides, these results predict that natural compounds simulating caterpillar traces may repel spider mites from agricultural crops.
Non-invasive screening of breast cancer from fingertip smears—a proof of concept study
Authors: Russo C. , Wyld L. , Da Costa Aubreu M. , Bury C. S. , Heaton C. , Cole L. M. , Francese S. 
Published: February 2023

AbstractBreast cancer is a global health issue affecting 2.3 million women per year, causing death in over 600,000. Mammography (and biopsy) is the gold standard for screening and diagnosis. Whilst effective, this test exposes individuals to radiation, has limitations to its sensitivity and specificity and may cause moderate to severe discomfort. Some women may also find this test culturally unacceptable. This proof-of-concept study, combining bottom-up proteomics with Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS) detection, explores the potential for a non-invasive technique for the early detection of breast cancer from fingertip smears. A cohort of 15 women with either benign breast disease (n = 5), early breast cancer (n = 5) or metastatic breast cancer (n = 5) were recruited from a single UK breast unit. Fingertips smears were taken from each patient and from each of the ten digits, either at the time of diagnosis or, for metastatic patients, during active treatment. A number of statistical analyses and machine learning approaches were investigated and applied to the resulting mass spectral dataset. The highest performing predictive method, a 3-class Multilayer Perceptron neural network, yielded an accuracy score of 97.8% when categorising unseen MALDI MS spectra as either the benign, early or metastatic cancer classes. These findings support the need for further research into the use of sweat deposits (in the form of fingertip smears or fingerprints) for non-invasive screening of breast cancer.
Chemistry: Reading and Writing the Book of Nature
Authors: Balzani Vincenzo , Venturi Margherita 
Published: February 2023

Many people are convinced that, among other courses taught in schools, chemistry is a difficult and complex subject. This view is often arrived at without justification. Setting out to introduce chemistry concepts and demystify chemistry, this book shows how it is a major part of our everyday lives. It introduces the readers into the wonderful world of atoms and molecules and chemical reactions whilst showing that chemistry is centrally important but also an emerging science and defines what the practising chemist does. The book also examines curiosity, creativity, fascination, poetry, beauty, and ethics in science.
Originally published in Italian, ‘Chimica – leggere e scrivere il libro della Natura’ was among the finalists of the 2013 Italian Award for popularization of science. The English translation has been sensitively delivered to explain concepts in simple language and emphasize the positive role that chemistry can play to shape our future.
Dust in Galaxies
Authors: Williams David A , Cecchi-Pestellini Cesare 
Published: February 2023

Without interstellar dust, the Universe as we see it today would not exist. Yet at first we considered this vital ingredient merely an irritating fog that prevented a clear view of the stars and nebulae in the Milky Way and other galaxies. We now know that interstellar dust has essential roles in the physics and chemistry of the formation of stars and planetary systems, the creation of the building blocks of life, and in the movement of those molecules to new planets. This is the story in this book.
After introducing the materials this interstellar dust is made of, the authors explain the range of sizes and shapes of the dust grains in the Milky Way galaxy and the life cycle of dust, starting from the origins of dust grains in stellar explosions through to their turbulent destruction. Later on we see the variety of processes in interstellar space involving dust and the events there that cause the dust to change in ways that astronomers and astrobiologists can use to indirectly observe those events.
This book is written for a general audience, concentrating on ideas rather than detailed mathematics and chemical formulae, and is the first time interstellar dust has been discussed at an accessible level.
The Science and Commerce of Whisky
Authors: Buxton Ian , Hughes Paul S 
Published: February 2023

Since the publication of the first edition in 2014, the whisky industry has continued to change. This book provides the reader with an overview of the latest academic research and industry best practice in an accessible and authoritative format. Despite the recession, new distillation capacity has been added at a record pace and new consumers in new markets have entered the arena. Distillers are experimenting with new finishes, packaging and marketing techniques and amongst consumers there is a hunger for knowledge and informed commentary. An entirely new chapter discussing the management and utilization of co-products and recent developments in areas such as anaerobic digestion is included along with revisions and updates to most chapters. Written by acknowledged and experienced authorities of the subject, this book provide an up to date treatment of this fast developing area. Aimed at the popular market, it provides a leading text for students of distilling, industry practitioners, new craft distillers and whisky enthusiasts.
Review of the 1st Edition
‘The authors have clearly put much effort into this book... I enjoyed the book almost as much as I enjoy whisky. Fascinating stuff from cover to cover.’ Ian W. Davies, Chromatographia, 2014, 77, 1733-1734
‘Sometimes, you come across a book that’s so comprehensive that it’s worth shouting about….a fascinating book that can be engaged with on numerous levels, even if you aren’t a student of distilling.
Pop it on the shelf and consult it from time to time over the coming years.
This might be the only whisky book you’ll ever need.’
http://malt-review.com/2014/08/01/book-review-the-science-and-commerce-of-whisky/