bluuebunny/crossref_metadata_2025_split huggingface dataset:
TraceTrack, an open-source software for batch processing, alignment and visualization of sanger sequencing chromatograms
Authors: Brazdilova Kveta , Prihoda David , Ton Quynh , Klock Heath , Bitton Danny A 
Published: July 2023

Abstract

Motivation
Despite the advent of next-generation sequencing technology and its widespread applications, Sanger sequencing remains instrumental for molecular biology subcloning work in biological and medical research and indispensable for drug discovery campaigns. Although Sanger sequencing technology has been long established, existing software for processing and visualization of trace file chromatograms is limited in terms of functionality, scalability and availability for commercial use.

Results
To fill this gap, we developed TraceTrack, an open-source web application tool for batch alignment, analysis and visualization of Sanger trace files. TraceTrack offers high-throughput matching of trace files to reference sequences, rapid identification of mutations and an intuitive chromatogram analysis. Comparative analysis between TraceTrack and existing software tools highlights the advantages of TraceTrack with regards to batch processing, visualization and export functionalities.

Availability and implementation
TraceTrack is available at https://github.com/MSDLLCpapers/TraceTrack and as a web application at https://tracetrack.dichlab.org. TraceTrack is a web application for batch processing and visualization of Sanger trace file chromatograms that meets the increasing demand of industrial sequence validation workflows in pharmaceutical settings.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
(m, n)-mer—a simple statistical feature for sequence classification
Authors: de Andrade Amanda Araújo Serrão , Grivet Marco , Brustolini Otávio , Vasconcelos Ana Tereza Ribeiro 
Published: July 2023

Abstract

Summary
The (m, n)-mer is a simple alternative classification feature based on conditional probability distributions. In this application note, we compared k-mer and (m, n)-mer frequency features in 11 distinct datasets used for binary, multiclass and clustering classifications. Our findings show that the (m, n)-mer frequency features are related to the highest performance metrics and often statistically outperformed the k-mers. Here, the (m, n)-mer frequencies improved performance for classifying smaller sequence lengths (as short as 300 bp) and yielded higher metrics when using short values of k (ranging from 2 to 4). Therefore, we present the (m, n)-mers frequencies to the scientific community as a feature that seems to be quite effective in identifying complex discriminatory patterns and classifying polyphyletic sequence groups.

Availability and implementation
The (m, n)-mer algorithm is released as an R package within the CRAN project (https://cran.r-project.org/web/packages/mnmer) and is also available at https://github.com/labinfo-lncc/mnmer.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Bold–shy continuum does not account for egg rejection behaviour in the Japanese tit
Authors: Shen Chao , Yu Jiangping , Yin Dake , Liu Qingzhen , Wang Haitao , Liang Wei 
Published: July 2023

AbstractIn response to brood parasitism, which significantly reduces the reproductive success of avian hosts, hosts have evolved the ability to recognize and reject parasitic eggs. Many studies have revealed the factors influencing egg recognition and egg rejection. Recent work has demonstrated that host personality along the bold–shy continuum can influence egg rejection behaviour. In addition, the egg rejection behaviour of hosts differs among populations, suggesting that individuals with different personalities might evolve various adaptive behaviours under different parasitic pressures, but there have been few relevant experiments to test this. In the present study, two populations of the Japanese tit, Parus minor, distributed in China were used to examine whether there were differences in egg rejection behaviour of individuals with different personalities. The results showed that egg rejection rates of bold individuals (which remained in the nest box when encountering human invaders) and shy individuals (which immediately flew away from the nest box when encountering human invaders) were similar in both populations of the Japanese tit, and there were also no significant differences in egg rejection rates between individuals of the same personality in the two populations. This study suggests that host personality along the bold–shy continuum does not account for egg rejection behaviour in Japanese tits. This might be attributable either to other factors that affect egg rejection behaviour counteracting the effect of personality or to the presence of multiple personality traits that act together in the Japanese tits, counteracting the effect of a single personality trait.
Peripherin is a biomarker of axonal damage in peripheral nervous system disease
Authors: Keddie Stephen , Smyth Duncan , Keh Ryan Y S , Chou Michael K L , Grant Donna , Surana Sunaina , Heslegrave Amanda , Zetterberg Henrik , Wieske Luuk , Michael Milou , Eftimov Filip , Bellanti Roberto , Rinaldi Simon , Hart Melanie S , Petzold Axel , Lunn Michael P 
Published: July 2023

Abstract
Valid, responsive blood biomarkers specific to peripheral nerve damage would improve management of peripheral nervous system (PNS) diseases. Neurofilament light chain (NfL) is sensitive for detecting axonal pathology but is not specific to PNS damage, as it is expressed throughout the PNS and CNS. Peripherin, another intermediate filament protein, is almost exclusively expressed in peripheral nerve axons. We postulated that peripherin would be a promising blood biomarker of PNS axonal damage.
We demonstrated that peripherin is distributed in sciatic nerve, and to a lesser extent spinal cord tissue lysates, but not in brain or extra-neural tissues. In the spinal cord, anti-peripherin antibody bound only to the primary cells of the periphery (anterior horn cells, motor axons and primary afferent sensory axons). In vitro models of antibody-mediated axonal and demyelinating nerve injury showed marked elevation of peripherin levels only in axonal damage and only a minimal rise in demyelination.
We developed an immunoassay using single molecule array technology for the detection of serum peripherin as a biomarker for PNS axonal damage. We examined longitudinal serum peripherin and NfL concentrations in individuals with Guillain-Barré syndrome (GBS, n = 45, 179 time points), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP, n = 35, 70 time points), multiple sclerosis (n = 30), dementia (as non-inflammatory CNS controls, n = 30) and healthy individuals (n = 24).
Peak peripherin levels were higher in GBS than all other groups (median 18.75 pg/ml versus &lt; 6.98 pg/ml, P &lt; 0.0001). Peak NfL was highest in GBS (median 220.8 pg/ml) and lowest in healthy controls (median 5.6 pg/ml), but NfL did not distinguish between CIDP (17.3 pg/ml), multiple sclerosis (21.5 pg/ml) and dementia (29.9 pg/ml). While peak NfL levels were higher with older age (rho = +0.39, P &lt; 0.0001), peak peripherin levels did not vary with age.
In GBS, local regression analysis of serial peripherin in the majority of individuals with three or more time points of data (16/25) displayed a rise-and-fall pattern with the highest value within the first week of initial assessment. Similar analysis of serial NfL concentrations showed a later peak at 16 days. Group analysis of serum peripherin and NfL levels in GBS and CIDP patients were not significantly associated with clinical data, but in some individuals with GBS, peripherin levels appeared to better reflect clinical outcome measure improvement.
Serum peripherin is a promising new, dynamic and specific biomarker of acute PNS axonal damage.
CDKL5 deficiency disorder: progressive brain atrophy may be part of the syndrome
Authors: Specchio Nicola , Trivisano Marina , Lenge Matteo , Ferretti Alessandro , Mei Davide , Parrini Elena , Napolitano Antonio , Rossi-Espagnet Camilla , Talenti Giacomo , Longo Daniela , Proietti Jacopo , Ragona Francesca , Freri Elena , Solazzi Roberta , Granata Tiziana , Darra Francesca , Bernardina Bernardo Dalla , Vigevano Federico , Guerrini Renzo 
Published: July 2023

Abstract
The clinical phenotype of Cyclin-Dependent Kinase-Like 5 (CDKL5) deficiency disorder (CDD) has been delineated but neuroimaging features have not been systematically analyzed. We studied brain magnetic resonance imaging (MRI) scans in a cohort of CDD patients and reviewed age at seizure onset, seizure semiology, head circumference. Thirty-five brain MRI from 22 unrelated patients were included. The median age at study entry was 13.4 years. In 14/22 patients (85.7%), MRI in the first year of life was unremarkable in all but two. In 11/22, we performed MRI after 24 months of age (range 2.5–23 years). In 8 out of 11 (72.7%), MRI showed supratentorial atrophy and in six cerebellar atrophy. Quantitative analysis detected volumetric reduction of the whole brain (−17.7%, P-value = 0.014), including both white matter (−25.7%, P-value = 0.005) and cortical gray matter (−9.1%, P-value = 0.098), with a reduction of surface area (−18.0%, P-value = 0.032), mainly involving the temporal regions, correlated with the head circumference (ρ = 0.79, P-value = 0.109). Both the qualitative structural assessment and the quantitative analysis detected brain volume reduction involving the gray and white matter. These neuroimaging findings may be related to either progressive changes due to CDD pathogenesis, or to the extreme severity of epilepsy, or both. Larger prospective studies are needed to clarify the bases for the structural changes we observed.
A Novel Method for Determination of Cyclobenzaprine in the Different Matrixes by UHPLC-DAD: Application to Real Human Plasma and Pharmaceutical Formulations
Authors: Akman Tugrul C 
Published: July 2023

Abstract
This study presents a novel and efficient method for determining of cyclobenzaprine (CBP) in human plasma and tablets using simple liquid–liquid microextraction and ultra-high performance liquid chromatography-diode-array detector. The developed method was optimized and validated for selectivity, linearity, precision, accuracy, limit of detection (LOD) and limit of quantification (LOQ). The chromatographic separation was achieved using a C18 column with a mobile phase consisting of a mixture of deionized water containing 0.1% TFA and methanol (30:70, v:v) at a flow rate of 1.0 mL/min. The extraction process provided high-efficiency recovery of CBP with a small plasma volume (%94.3). The method showed good linearity within the concentration range of 0.005–10 μg/mL, with a correlation coefficient of 0.999. The LOD and LOQ values were found to be 0.0013 and 0.005 μg/mL, respectively. The intra- and inter-day %RSD were &lt;8%, and %RE were ranged from −0.50 to 0.01%. The proposed method was successfully applied to the analysis of CBP in real human plasma samples and tablets, indicating its applicability in clinical and pharmaceutical research. In conclusion, the simple, low cost, high sensitivity and rapid nature of this method make it an attractive option for the quantification of CBP in human plasma and pharmaceutical dosage forms.
Prognostic value of peripheral endothelial function on major adverse cardiovascular events above traditional risk factors
Authors: Rajai Nazanin , Toya Takumi , Sara Jaskanwal D , Rajotia Arush , Lopez-Jimenez Francisco , Lerman Lilach O , Lerman Amir 
Published: July 2023

Abstract

Aims
This study aims to identify whether adding peripheral microvascular dysfunction (PMED), a marker of atherosclerosis to established risk scores has an incremental prognostic value for major adverse cardiovascular events (MACE).

Methods and results
This is a retrospective study of patients who underwent measuring peripheral arterial tonometry from 2006 to 2020. The optimal cut-off value of the reactive hyperaemia index (RHI) that had maximal prognostic value associated with MACE was calculated. Peripheral microvascular endothelial dysfunction was defined as the RHI lower than the cut-off. Traditional cardiovascular risk factors such as age, sex, congestive heart failure, hypertension, diabetes, stroke, and vascular disease were determined to calculate the CHA2DS2-Vasc score. The outcome was MACE defined as myocardial infarction, heart failure hospitalization, cerebrovascular events, and all-cause mortality. A total of 1460 patients were enrolled (average age 51.4 ± 13.6, 64.1% female). The optimal cut-off value of the RHI was 1.83 in the overall population and in females and males was 1.61 and 1.8, respectively. The risk of MACE during 7 [interquartile range (IQR): 5,11] years of follow-up was 11.2%. Kaplan–Meier analysis showed that lower RHI is associated with worse MACE-free survival (P &lt; 0.001). Multivariate Cox proportional hazard analysis, controlling for classic cardiovascular risk factors or risk scores such as CHA2DS2-Vasc and Framingham risk score revealed that PMED is an independent predictor of MACE.

Conclusion
Peripheral microvascular dysfunction predicts cardiovascular events. Non-invasive assessment of peripheral endothelial function may be useful in early detection and improving the stratification of high-risk patients for cardiovascular events.

Lay summary

Key findings
GWLD: an R package for genome-wide linkage disequilibrium analysis
Authors: Zhang Rong , Wu Huaxuan , Li Yasai , Huang Zehang , Yin Zongjun , Yang Cai-Xia , Du Zhi-Qiang 
Published: July 2023

Abstract
Linkage disequilibrium (LD) analysis is fundamental to the investigation of the genetic architecture of complex traits (e.g. human disease, animal and plant breeding) and population structure and evolution dynamics. However, until now, studies primarily focus on LD status between genetic variants located on the same chromosome. Moreover, genome (re)sequencing produces unprecedented numbers of genetic variants, and fast LD computation becomes a challenge. Here, we have developed GWLD, a parallelized and generalized tool designed for the rapid genome-wide calculation of LD values, including conventional D/D′, r2, and (reduced) mutual information (MI and RMI) measures. LD between genetic variants within and across chromosomes can be rapidly computed and visualized in either an R package or a standalone C++ software package. To evaluate the accuracy and speed of LD calculation, we conducted comparisons using 4 real datasets. Interchromosomal LD patterns observed potentially reflect levels of selection intensity across different species. Both versions of GWLD, the R package (https://github.com/Rong-Zh/GWLD/tree/master/GWLD-R) and the standalone C++ software (https://github.com/Rong-Zh/GWLD/tree/master/GWLD-C%2B%2B), are freely available on GitHub.
Queering the Responsibility to Protect
Authors: Gifkins Jess , Cooper-Cunningham Dean 
Published: July 2023

Abstract
Research on the Responsibility to Protect has become increasingly intersectional with over two decades of research; however, there remains a blind spot on the persecution of queer people. This is surprising given that queer people have been persecuted in atrocity crimes as far back as the Holocaust. While the field of genocide studies has recently begun to engage with this area, we frame queer persecution more broadly around the four R2P crimes. In this article we set out the rationale and urgency for including a queer lens in the prevention of atrocity crimes. This is not only about a focus on queer people; we argue for a queer politics and ethics that ceaselessly interrogates all relations of power. We outline the scale of the gap in academic research, policy and state understandings of R2P. Since R2P is often framed as a foreign policy matter by western states, with the global South as the object of R2P, we include two case-studies on escalating persecution against LGBTI+ people in Europe: the United Kingdom and Hungary. We argue that the R2P research and policy communities should remove what we call the ‘cishetronormative blindfold’ and engage more broadly with intersectional approaches to atrocity prevention.
The ‘subaltern speak’: can we, the experts, listen?
Authors: Behera Navnita Chadha 
Published: July 2023

Abstract
Knowledge production in peace and conflict research is marked by a disconnect between its ‘expertise-driven’ research inquiries and lived realities of people across the world. In focusing on what knowledge and whose knowledge counts as legitimate among the diverse stakeholders, the article locates the raison d'être of this gap in the epistemic erasures inflicted by imperial knowledge and its lasting legacies, especially that of privileging the primacy and autonomy of the political over the social institutions in maintaining order. This, along with the limiting epistemes of western modernity explain the state-centrism in governmental and academic expertise, especially in post-colonial societies. The article makes a case for historicizing and decolonizing its epistemes and tools of research, and illustrates how this can be done by drawing on the Kashmir conflict as it unfolded in the early 1990s in the Indian part of Jammu and Kashmir state. In a point of departure from the much-acclaimed question asked by Gayatri Spivak: ‘can the subaltern speak?’, the article argues that the subaltern can speak and has indeed never been silent. So, the question it poses is: can we, the experts, listen?
Two Ways of Representing Specialist Knowledge: Analysing the Botanical Lexicon in Diccionario de la Lengua Española and Diccionario del Español de México
Authors: Camacho-Niño Jesús 
Published: July 2023

Abstract
This article explores the lexicographic codification of botanical knowledge in two general dictionaries: Diccionario de la lengua española (2014 [2021]), produced by the Real Academia Española in Spain, and Diccionario del español de México (2019), published by El Colegio de México. It begins with a historical overview of the inclusion of botanical terminology in general dictionaries by the Real Academia Española and by other authors. Then, it analyses the degree to which the botanical terms included in each dictionary meet the inclusion criteria established. Finally, it focuses on diatechnical labelling and the differences between the two dictionaries in terms of the disciplines to which terms are assigned. This allows us to draw conclusions regarding the representation of this field of knowledge in the two dictionaries and the lexicographic techniques used to produce them.
An Algorithm for Berenstein–Kazhdan Decoration Functions and Trails for Classical Lie Algebras
Authors: Kanakubo Yuki , Koshevoy Gleb , Nakashima Toshiki 
Published: July 2023

Abstract
For a simply connected connected simple algebraic group $G$, it is known that a variety $B_{w_0}^-:=B^-\cap U\overline{w_0}U$ has a geometric crystal structure with a positive structure $\theta ^-_{\textbf{i}}:(\mathbb{C}^{\times })^{l(w_0)}\rightarrow B_{w_0}^-$ for each reduced word $\textbf{i}$ of the longest element $w_0$ of Weyl group. A rational function $\Phi ^h_{BK}=\sum _{i\in I}\Delta _{w_0\Lambda _i,s_i\Lambda _i}$ on $B_{w_0}^-$ is called a half-potential, where $\Delta _{w_0\Lambda _i,s_i\Lambda _i}$ is a generalized minor. Computing $\Phi ^h_{BK}\circ \theta ^-_{\textbf{i}}$ explicitly, we get an explicit form of string cone or polyhedral realization of $B(\infty )$ for the finite dimensional simple Lie algebra $\mathfrak{g}=\textrm{Lie}(G)$. In this paper, for an arbitrary reduced word $\textbf{i}$, we give an algorithm to compute the summand $\Delta _{w_0\Lambda _i,s_i\Lambda _i}\circ \theta ^-_{\textbf{i}}$ of $\Phi ^h_{BK}\circ \theta ^-_{\textbf{i}}$ in the case $i\in I$ satisfies that for any weight $\mu $ of $V(-w_0\Lambda _i)$ and $t\in I$, it holds $\langle h_t,\mu \rangle \in \{2,1,0,-1,-2\}$. In particular, if $\mathfrak{g}$ is of type $\textrm{A}_n$, $\textrm{B}_n$, $\textrm{C}_n$ or $\textrm{D}_n$ then all $i\in I$ satisfy this condition so that one can completely calculate $\Phi ^h_{BK}\circ \theta ^-_{\textbf{i}}$. We will also prove that our algorithm works in the case $\mathfrak{g}$ is of type $\textrm{G}_2$.
A call for better validation of opioid overdose risk algorithms
Authors: McElfresh Duncan C , Chen Lucia , Oliva Elizabeth , Joyce Vilija , Rose Sherri , Tamang Suzanne 
Published: July 2023

Abstract
Clinical decision support (CDS) systems powered by predictive models have the potential to improve the accuracy and efficiency of clinical decision-making. However, without sufficient validation, these systems have the potential to mislead clinicians and harm patients. This is especially true for CDS systems used by opioid prescribers and dispensers, where a flawed prediction can directly harm patients. To prevent these harms, regulators and researchers have proposed guidance for validating predictive models and CDS systems. However, this guidance is not universally followed and is not required by law. We call on CDS developers, deployers, and users to hold these systems to higher standards of clinical and technical validation. We provide a case study on two CDS systems deployed on a national scale in the United States for predicting a patient’s risk of adverse opioid-related events: the Stratification Tool for Opioid Risk Mitigation (STORM), used by the Veterans Health Administration, and NarxCare, a commercial system.
FHIR-up! Advancing knowledge from clinical data through application of standardized nursing terminologies within HL7® FHIR®
Authors: Monsen Karen A , Heermann Laura , Dunn-Lopez Karen 
Published: July 2023

Abstract
Health Level 7®’s (HL7) Fast Healthcare Interoperability Resources® (FHIR®) is leading new efforts to make data available to healthcare clinicians, administrators, and leaders. Standardized nursing terminologies were developed to enable nursing’s voice and perspective to be visible within the healthcare data ecosystem. The use of these SNTs has been shown to improve care quality and outcomes, and to provide data for knowledge discovery. The role of SNTs in describing assessments and interventions and measuring outcomes is unique in health care, and synergistic with the purpose and goals of FHIR. FHIR acknowledges nursing as a discipline of interest and yet the use of SNTs within the FHIR ecosystem is rare. The purpose of this article is to describe FHIR, SNTs, and the potential for synergy in the use of SNTs with FHIR. Toward improving understanding how FHIR works to transport and store knowledge and how SNTs work to convey meaning, we provide a framework and examples of SNTs and their coding for use within FHIR solutions. Finally, we offer recommendations for the next steps to advance FHIR-SNT collaboration. Such collaboration will advance both nursing specifically and health care in general, and most importantly, improve population health.