bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colon or semicolon: gut sampling microdevices for omics insights
Authors: Nagpal Sunil , Srivastava Sarvesh Kumar 
Published: October 2024

AbstractIngestible microdevices represent a breakthrough in non-invasive sampling of the human gastrointestinal (GI) tract. By capturing the native spatiotemporal microbiome and intricate biochemical gradients, these devices allow a non-invasive multi-omic access to the unperturbed host-microbiota crosstalk, immune/nutritional landscapes and gut-organ connections. We present the current progress of GI sampling microdevices towards personalized metabolism and fostering collaboration among clinicians, engineers, and data scientists.
Predicting visual function by interpreting a neuronal wiring diagram
Authors: Seung H. Sebastian 
Published: October 2024

AbstractAs connectomics advances, it will become commonplace to know far more about the structure of a nervous system than about its function. The starting point for many investigations will become neuronal wiring diagrams, which will be interpreted to make theoretical predictions about function. Here I demonstrate this emerging approach with the Drosophila optic lobe, analysing its structure to predict that three Dm3 (refs. 1–4) and three TmY (refs. 2,4) cell types are part of a circuit that serves the function of form vision. Receptive fields are predicted from connectivity, and suggest that the cell types encode the local orientation of a visual stimulus. Extraclassical5,6 receptive fields are also predicted, with implications for robust orientation tuning7, position invariance8,9 and completion of noisy or illusory contours10,11. The TmY types synapse onto neurons that project from the optic lobe to the central brain12,13, which are conjectured to compute conjunctions and disjunctions of oriented features. My predictions can be tested through neurophysiology, which would constrain the parameters and biophysical mechanisms in neural network models of fly vision14.
Neuronal parts list and wiring diagram for a visual system
Authors: Matsliah Arie , Yu Szi-chieh , Kruk Krzysztof , Bland Doug , Burke Austin T. , Gager Jay , Hebditch James , Silverman Ben , Willie Kyle Patrick , Willie Ryan , Sorek Marissa , Sterling Amy R. , Kind Emil , Garner Dustin , Sancer Gizem , Wernet Mathias F. , Kim Sung Soo , Murthy Mala , Seung H. Sebastian ,   The FlyWire Consortium, David Celia , Joroff Jenna , Kristiansen Anne , Stocks Thomas , Braun Amalia , Silies Marion , Skelton Jaime , Aiken Travis R. , Ioannidou Maria , Collie Matt , Linneweber Gerit A. , Molina-Obando Sebastian , Dorkenwald Sven , Panes Nelsie , Gogo Allien Mae , Rastgarmoghaddam Dorfam , Pilapil Cathy , Candilada Rey Adrian , Serafetinidis Nikitas , Lee Wei-Chung , Borst Alexander , Wilson Rachel I. , Schlegel Philipp , Jefferis Gregory S. X. E. 
Published: October 2024

AbstractA catalogue of neuronal cell types has often been called a ‘parts list’ of the brain1, and regarded as a prerequisite for understanding brain function2,3. In the optic lobe of Drosophila, rules of connectivity between cell types have already proven to be essential for understanding fly vision4,5. Here we analyse the fly connectome to complete the list of cell types intrinsic to the optic lobe, as well as the rules governing their connectivity. Most new cell types contain 10 to 100 cells, and integrate information over medium distances in the visual field. Some existing type families (Tm, Li, and LPi)6–10 at least double in number of types. A new serpentine medulla (Sm) interneuron family contains more types than any other. Three families of cross-neuropil types are revealed. The consistency of types is demonstrated by analysing the distances in high-dimensional feature space, and is further validated by algorithms that select small subsets of discriminative features. We use connectivity to hypothesize about the functional roles of cell types in motion, object and colour vision. Connectivity with ‘boundary types’ that straddle the optic lobe and central brain is also quantified. We showcase the advantages of connectomic cell typing: complete and unbiased sampling, a rich array of features based on connectivity and reduction of the connectome to a substantially simpler wiring diagram of cell types, with immediate relevance for brain function and development.
The fly connectome reveals a path to the effectome
Authors: Pospisil Dean A. , Aragon Max J. , Dorkenwald Sven , Matsliah Arie , Sterling Amy R. , Schlegel Philipp , Yu Szi-chieh , McKellar Claire E. , Costa Marta , Eichler Katharina , Jefferis Gregory S. X. E. , Murthy Mala , Pillow Jonathan W. 
Published: October 2024

AbstractA goal of neuroscience is to obtain a causal model of the nervous system. The recently reported whole-brain fly connectome1–3 specifies the synaptic paths by which neurons can affect each other, but not how strongly they do affect each other in vivo. To overcome this limitation, we introduce a combined experimental and statistical strategy for efficiently learning a causal model of the fly brain, which we refer to as the ‘effectome’. Specifically, we propose an estimator for a linear dynamical model of the fly brain that uses stochastic optogenetic perturbation data to estimate causal effects and the connectome as a prior to greatly improve estimation efficiency. We validate our estimator in connectome-based linear simulations and show that it recovers a linear approximation to the nonlinear dynamics of more biophysically realistic simulations. We then analyse the connectome to propose circuits that dominate the dynamics of the fly nervous system. We discover that the dominant circuits involve only relatively small populations of neurons—thus, neuron-level imaging, stimulation and identification are feasible. This approach also re-discovers known circuits and generates testable hypotheses about their dynamics. Overall, we provide evidence that fly whole-brain dynamics are generated by a large collection of small circuits that operate largely independently of each other. This implies that a causal model of a brain can be feasibly obtained in the fly.
Human DUS1L catalyzes dihydrouridine modification at tRNA positions 16/17, and DUS1L overexpression perturbs translation
Authors: Matsuura Jin , Akichika Shinichiro , Wei Fan-Yan , Suzuki Tsutomu , Yamamoto Takahiro , Watanabe Yuka , Valášek Leoš Shivaya , Mukasa Akitake , Tomizawa Kazuhito , Chujo Takeshi 
Published: October 2024

AbstractHuman cytoplasmic tRNAs contain dihydrouridine modifications at positions 16 and 17 (D16/D17). The enzyme responsible for D16/D17 formation and its cellular roles remain elusive. Here, we identify DUS1L as the human tRNA D16/D17 writer. DUS1L knockout in the glioblastoma cell lines LNZ308 and U87 causes loss of D16/D17. D formation is reconstituted in vitro using recombinant DUS1L in the presence of NADPH or NADH. DUS1L knockout/overexpression in LNZ308 cells shows that DUS1L supports cell growth. Moreover, higher DUS1L expression in glioma patients is associated with poorer prognosis. Upon vector-mediated DUS1L overexpression in LNZ308 cells, 5′ and 3′ processing of precursor tRNATyr(GUA) is inhibited, resulting in a reduced mature tRNATyr(GUA) level, reduced translation of the tyrosine codons UAC and UAU, and reduced translational readthrough of the near-cognate stop codons UAA and UAG. Moreover, DUS1L overexpression increases the amounts of several D16/D17-containing tRNAs and total cellular translation. Our study identifies a human dihydrouridine writer, providing the foundation to study its roles in health and disease.
SCAR-6 elncRNA locus epigenetically regulates PROZ and modulates coagulation and vascular function
Authors: Ranjan Gyan , Sehgal Paras , Scaria Vinod , Sivasubbu Sridhar 
Published: October 2024

AbstractIn this study, we characterize a novel lncRNA-producing gene locus that we name Syntenic Cardiovascular Conserved Region-Associated lncRNA-6 (scar-6) and functionally validate its role in coagulation and cardiovascular function. A 12-bp deletion of the scar-6 locus in zebrafish (scar-6gib007Δ12/Δ12) results in cranial hemorrhage and vascular permeability. Overexpression, knockdown and rescue with the scar-6 lncRNA modulates hemostasis in zebrafish. Molecular investigation reveals that the scar-6 lncRNA acts as an enhancer lncRNA (elncRNA), and controls the expression of prozb, an inhibitor of factor Xa, through an enhancer element in the scar-6 locus. The scar-6 locus suppresses loop formation between prozb and scar-6 sequences, which might be facilitated by the methylation of CpG islands via the prdm14-PRC2 complex whose binding to the locus might be stabilized by the scar-6 elncRNA transcript. Binding of prdm14 to the scar-6 locus is impaired in scar-6gib007Δ12/Δ12 zebrafish. Finally, activation of the PAR2 receptor in scar-6gib007Δ12/Δ12 zebrafish triggers NF-κB-mediated endothelial cell activation, leading to vascular dysfunction and hemorrhage. We present evidence that the scar-6 locus plays a role in regulating the expression of the coagulation cascade gene prozb and maintains vascular homeostasis.
Complex regulation of tau phosphorylation by the endothelin system in brain microvascular endothelial cells (BMVECs): link to barrier function
Authors: Karakaya Eda , Abdul Yasir , Edwards Jazlyn , Jamil Sarah , Albayram Onder , Ergul Adviye 
Published: October 2024

Abstract
Endothelin-1 (ET-1), the most potent vasoconstrictor identified to date, contributes to cerebrovascular dysfunction. ET-1 levels in postmortem brain specimens from individuals diagnosed with Alzheimer’s disease (AD) and related dementias (ADRD) were shown to be related to cerebral hypoxia and disease severity. ET-1-mediated vascular dysfunction and ensuing cognitive deficits have also been reported in experimental models of AD and ADRD. Moreover, studies also showed that ET-1 secreted from brain microvascular endothelial cells (BMVECs) can affect neurovascular unit integrity in an autocrine and paracrine manner. Vascular contributions to cognitive impairment and dementia (VCID) is a leading ADRD cause known to be free of neuronal tau pathology, a hallmark of AD. However, a recent study reported cytotoxic hyperphosphorylated tau (p-tau) accumulation, which fails to bind or stabilize microtubules in BMVECs in VCID. Thus, the study aimed to determine the impact of ET-1 on tau pathology, microtubule organization, and barrier function in BMVECs. Cells were stimulated with 1 μM ET-1 for 24 h in the presence/absence of ETA (BQ123; 20 μM) or ETB (BQ788; 20 μM) receptor antagonists. Cell lysates were assayed for an array of phosphorylation site-specific antibodies and microtubule organization/stabilization markers. ET-1 stimulation increased p-tau Thr231 but decreased p-tau Ser199, Ser262, Ser396, and Ser214 levels only in the presence of ETA or ETB antagonism. ET-1 also impaired barrier function in the presence of ETA antagonism. These novel findings suggest that (1) dysregulation of endothelial tau phosphorylation may contribute to cerebral microvascular dysfunction and (2) the ET system may be an early intervention target to prevent hyperphosphorylated tau-mediated disruption of BMVEC barrier function.
Solar internetwork magnetic fields: Statistical comparison between observations and MHD simulations
Authors: Ebert E. , Milić I. , Borrero J. M. 
Published: October 2024

Context. Although the magnetic fields in the quiet Sun account for the majority of the magnetic energy in the solar photosphere, inferring their exact spatial distribution, origin, and evolution poses an important challenge because the signals lie at the limit of today’s instrumental precision. This severely hinders and biases our interpretations, which are mostly made through nonlinear model-fitting approaches.
Aims. Our goal is to directly compare simulated and observed polarization signals in the Fe I 6301 Å and 6302 Å spectral lines in the very quiet Sun, the so-called solar internetwork (IN). This way, we aim to constrain the mechanism responsible for the generation of the quiet Sun magnetism while avoiding the biases that plague other diagnostic methods.
Methods. We used three different three-dimensional radiative magneto-hydrodynamic simulations representing different scenarios of magnetic field generation in the internetwork: small-scale dynamo, decay of active regions, and horizontal flux emergence. We synthesized Stokes profiles at different viewing angles and degraded them according to the instrumental specifications of the spectro-polarimeter (SP) on board the Hinode satellite. Finally, we statistically compared the simulated spectra to the Hinode/SOT/SP observations at the appropriate viewing angles.
Results. Of the three simulations, the small-scale dynamo best reproduced the statistical properties of the observed polarization signals. This is especially prominent for the disk center viewing geometry, where the agreement is excellent. Moving toward more inclined lines of sight, the agreement worsens slightly.
Conclusions The agreement between the small-scale dynamo simulation and observations at the disk center suggests that small-scale dynamo action plays an important role in the generation of quiet Sun magnetism. However, the magnetic field around 50 km above the continuum layer in this simulation does not reproduce observations as well as at the very base of the photosphere.
Chemical composition of planetary hosts
Authors: Sharma A. , Stonkutė E. , Drazdauska A. , Minkevičiūtė R. , Mikolaitis Š. , Tautvaišienė G. , Narbuntas T. 
Published: October 2024

Context. Accurate atmospheric parameters and chemical composition of planet hosts play a major role in characterising exoplanets and understanding their formation and evolution.
Aims. Our objective is to uniformly determine atmospheric parameters and chemical abundances of carbon (C), nitrogen (N), oxygen(O), and the α-elements, magnesium (Mg) and silicon (Si), along with C/O, N/O and Mg/Si abundance ratios for planet-hosting stars. In this analysis, we aim to investigate the potential links between stellar chemistry and the presence of planets.
Methods. Our study is based on high-resolution spectra of 149 F, G, and K dwarf and giant stars hosting planets or planetary systems. The spectra were obtained with the Vilnius University Echelle Spectrograph (VUES) on the 1.65 m Molėtai Observatory telescope. The determination of stellar parameters was based on a standard analysis using equivalent widths and one-dimensional, plane-parallel model atmospheres calculated under the assumption of local thermodynamical equilibrium. The differential synthetic spectrum method was used to uniformly determine the carbon C(C2), nitrogen N(CN), oxygen [O I], magnesium Mg I, and silicon Si I elemental abundances as well as the C/O, N/O, and Mg/Si ratios.
Results. We analysed elemental abundances and ratios in dwarf and giant stars, finding that [C/Fe], [O/Fe], and [Mg/Fe] are lower in metal-rich dwarf hosts; whereas [N/Fe] is close to the Solar ratio. Giants show smaller scatter in [C/Fe] and [O/Fe] and lower than the Solar average [C/Fe] and C/O ratios. The (C+N+O) abundances increase with [Fe/H] in giant stars, with a minimal scatter. We also noted an overabundance of Mg and Si in planet-hosting stars, particularly at lower metallicities, and a lower Mg/Si ratio in stars with planets. In giants hosting high-mass planets, nitrogen shows a moderate positive relationship with planet mass. C/O and N/O ratios show moderate negative and positive slopes in giant stars, respectively. The Mg/Si ratio shows a negative correlation with planet mass across the entire stellar sample.
Design of composite optical nanofibers for new all-solid-state Raman wavelength converters
Authors: Lebrun Sylvie , Bouhadida Maha , Dampt Théo , Fauvel Mathieu , Larat Christian , Azzoune Abderrahim , Beugnot Jean-Charles , Divay Laurent 
Published: October 2024

We present the design of composite optical nanofibers (ONF) coated with thin layers of nonlinear materials, Titanium dioxyde (TiO2) and Polymethyl methacrylate (PMMA), for the realization of new all-solid Raman wavelength converters for an emission around 1.5 μm. Our simulations show that Stimulated Raman Scattering can be obtained with moderate input peak powers, typical ONF geometrical parameters, and layer thicknesses deposited which are technologically achievable: a few tens of nm for TiO2 and a few hundreds of nm for PMMA. This study enlarges the field of applications of ONF in nonlinear optics and lasers by opening the way to the coating by other materials such as doped polymers.
21-Hydroxylase Deficiency Detected in Neonatal Screening: High
Probability of False Negativity in Late Onset Form
Authors: David Jan , Hrubá Zuzana , Vinohradská Hana , Hedelová Monika , Fialová Alena , Votava Felix 
Published: October 2024

Abstract
Aim Despite the high sensitivity of neonatal screening in detecting the
classical form of congenital adrenal hyperplasia due to 21-hydroxylase
deficiency, one of the unclear issues is identifying asymptomatic children with
late onset forms. The aim of this nationwide study was to analyse the
association between genotype and screened level of 17-hydroxyprogesterone in
patients with the late onset form of 21-hydroxylase deficiency and to quantify
false negativity.
Methods In the Czech Republic, 1,866,129 neonates were screened
(2006–2022). Among this cohort, 159 patients were confirmed to suffer from
21-hydroxylase deficiency, employing the 17-hydroxyprogesterone
birthweight/gestational age-adjusted cut-off limits, and followed by the genetic
confirmation. The screening prevalence was 1:11,737. Another 57 patients who
were false negative in neonatal screening were added to this cohort based on
later diagnosis by clinical suspicion. To our knowledge, such a huge nationwide
cohort of false negative patients has not been documented before.
Results Overall, 57 patients escaped from neonatal screening in the
monitored period. All false negative patients had milder forms. Only one patient
had simple virilising form and 56 patients had the late onset form. The
probability of false negativity in the late onset form was 76.7%. The difference
in 17-hydroxyprogesterone screening values was statistically significant
(p<0.001) between severe forms (median 478.8 nmol/L) and milder (36.2 nmol/L)
forms. Interestingly, the higher proportion of females with milder forms was
statistically significant compared with the general population.
Conclusions A negative neonatal screening result does not exclude milder
forms of 21-hydroxylase deficiency during the differential diagnostic procedure
of children with precocious pseudopuberty.
Evaluation of Treatment and Recurrence-Free Survival in Patients with Early HER2-Positive Breast Cancer: Real-Life Data Comparing Public and Private Healthcare
Authors: Capella Mariana Pilon , Lealdini Viviane , Aguiar Pedro 
Published: October 2024

Abstract
Introduction The present study was designed to compare the treatment provided in private and public health care facilities for women positive for early breast cancer of the human epidermal growth factor receptor 2 (HER2) subtype, who received anti-HER2 therapy in neoadjuvant or adjuvant settings, with an evaluation of the recurrence-free survival (RFS) and pathological complete response (pCR) rates.
Materials and Methods The current is a retrospective study carried out at the Instituto Brasileiro de Controle do Cancer (IBCC Oncologia), in the city of São Paulo, Brazil. We included patients treated between 2015 and 2020.
Results The study included 472 medical records of early HER2-positive breast cancer patients treated in the public and private health care systems who received neoadjuvant or adjuvant treatments. The pathological complete response (pCR) was related to a lower recurrence rate and a longer recurrence-free survival (RFS). The results showed no statistically significant difference between the public and private health care systems in terms of RFS.
Discussion Although the public health care patients were diagnosed with more advanced diseases than the private health care patients, both presented similar survival rates. In spite of the small number of patients evaluated, the dual HER2 blockade did not improve the clinical outcomes. These findings should be confirmed through studies with a larger number of patients and a longer follow-up period.
15.8.3 Naphthyridines (Update 2024)
Authors: Walker J. C. L. 
Published: October 2024

Abstract
This review is an update to the earlier Science of Synthesis contribution describing methods for the synthesis of naphthyridines. It focuses on the literature published in the period 2005–2023. Naphthyridines are widely used compounds with a broad range of applications, for example, in active pharmaceutical ingredients and as ligands for metal-based catalysts.
20.2.11.2 Alk-2-enoic Acids (Update 2024)
Authors: Durandetti M. , Franck X. 
Published: October 2024

Abstract
The α, β-unsaturated carboxylic acid motif stands out for its versatility and utility in constructing complex molecular structures, spanning pharmaceuticals to natural products. This review describes the published methods for the synthesis of alk-2-enoic acids reported between 2007 and 2023. It is an update to the original Science of Synthesis review (Section 20.2.11), published in 2007. The focus lies on novel synthetic approaches facilitating the incorporation of the α, β-unsaturated carboxylic acid motif from a range of starting materials, including diversely functionalized or unfunctionalized alcohols, aldehydes, ketones, alkenes, and alkynes.
7 Photocatalysis in Chemical Biology
Authors: Kohyama A. , Winssinger N. 
Published: October 2024

AbstractControlling the space and time of chemical processes has led to great benefits in biological research. From this perspective, photocatalytic reactions have been developed to be a breakthrough in chemical biology. In combination with a photocatalyst, visible-light irradiation turns on the reaction system by converting an inactive species into an active one. This review showcases the principle of photocatalytic reactions and some applications in chemical biology by focusing on the cooperative use of active species and proximity effects.
A thousand tiny theories: The colonized subject, postcolonial literature, and decolonial epistemologies
Authors: Greedharry Mrinalini 
Published: October 2024

AbstractPsychoanalysis has, from its origins, made a claim to superior interpretative knowledge of literature than literary studies itself, often using its knowledge of literature to affirm and reaffirm its own colonial logics. In this paper, I examine how this colonial epistemological position is reaffirmed in literary interpretations of postcolonial and decolonial writing, even as psychosocial studies works to decolonize the psy disciplines. Through discussion of Dangarembga’s Nervous Conditions trilogy, I argue instead that postcolonial writing offers its own autotheory of the colonized mind which opens a pathway to decolonizing the authority of the psy disciplines.