Miracle-dz/UniFAR-FTUs huggingface dataset:
Carbon‐cycle feedbacks of changes in the Atlantic meridional overturning circulation under future atmospheric CO2

An Earth System model of intermediate complexity is used to quantify the effects of potential reorganizations of the Atlantic meridional overturning circulation, ranging from a weakening to a complete shutdown, on future uptake of excess CO2 by the ocean and the terrestrial biosphere. Circulation changes significantly reduce oceanic CO2 uptake, with the largest effects occurring under a complete shutdown. The reduction in uptake is caused to a large extent by a decline in marine export of organic particulate matter. On land, soil carbon increases because of reduced soil respiration in the mid‐latitudes of the Northern Hemisphere. This gain is partially compensated by loss of vegetation carbon associated with reduced primary production in the northern high latitudes due to a cooler and dryer climate. Altogether, these processes act to modestly enhance CO2 concentration levels in the atmosphere, thereby leading to a small positive feedback. The rise in atmospheric CO2 ranges from 13 ppm to 34 ppm in 2500, depending on the amount of AMOC weakening, the magnitude of the anthropogenic CO2 perturbation, and the future CO2 fertilization effect.
Fluorescence cholangiography for laparoscopic cholecystectomy: how, when, and why? A single-center preliminary study

Abstract Introduction Bile duct injuries avoidance is a key goal of biliary surgery. In this prospective study we evaluate the safety and feasibility of ICG fluorescent cholangiography during laparoscopic cholecystectomy (LC) focusing on the optimization of timing and dose administration. Material and methods From February to December 2022 fifty-four LC were performed with fluorescence imaging in our surgical department. 2.5 mg ICG were administered intravenously between 5 h and 24 h before surgery. Near-infrared fluorescent cholangiography (NIRF-C) was performed. Adequate fluorescence was evaluated by comparing agent accumulation in the gallbladder and the extrahepatic duct and the background of liver parenchyma. Results Biliary anatomy was identified in all cases. Median time of ICG administration was 11 h previous surgery and three groups of patients were identified: group A receiving ICG 5–9 h, group B 10–14 h, group C 15–24 h before surgery. Peak contrast was gained in group B, with minimal fluorescence of liver parenchyma and more intense visibility of the biliary tract. Intraoperative cholangiogram was unnecessary in all cases. Conclusion Fluorescent cholangiography during LC is safe and feasible overcoming the limits of other techniques available. 2.5 mg ICG administered 10–14 h before surgery produces optimal outcomes for near-infrared (NIR) fluorescent cholangiography.
Estimation of dispersion in orientations of natural fractures from seismic data: Application to DFN modeling and flow simulation

This article describes a statistical methodology to estimate dominant fracture orientation and dispersion from seismically calculated 3D structural attributes. The orientation-dispersion parameter is a modified version of the circular variance that is independent of direction and can be used to compute the Fisher coefficient, a key parameter in the probability density function used in discrete-fracture-network (DFN) modeling to stochastically generate fracture orientations. We show examples of applications to seismic-constrained DFN modeling and perform flow simulations on fractured models built using different dispersion-parameter models to discuss possible implications for drainage of naturally fractured unconventional reservoirs.
Trichothiodystrophy‐associated MPLKIP maintains DBR1 levels for proper lariat debranching and ectodermal differentiation

The brittle hair syndrome Trichothiodystrophy (TTD) is characterized by variable clinical features, including photosensitivity, ichthyosis, growth retardation, microcephaly, intellectual disability, hypogonadism, and anaemia. TTD‐associated mutations typically cause unstable mutant proteins involved in various steps of gene expression, severely reducing steady‐state mutant protein levels. However, to date, no such link to instability of gene‐expression factors for TTD‐associated mutations in MPLKIP/TTDN1 has been established. Here, we present seven additional TTD individuals with MPLKIP mutations from five consanguineous families, with a newly identified MPLKIP variant in one family. By mass spectrometry‐based interaction proteomics, we demonstrate that MPLKIP interacts with core splicing factors and the lariat debranching protein DBR1. MPLKIP‐deficient primary fibroblasts have reduced steady‐state DBR1 protein levels. Using Human Skin Equivalents (HSEs), we observed impaired keratinocyte differentiation associated with compromised splicing and eventually, an imbalanced proteome affecting skin development and, interestingly, also the immune system. Our data show that MPLKIP, through its DBR1 stabilizing role, is implicated in mRNA splicing, which is of particular importance in highly differentiated tissue.
Validation of the Xpert Breast Cancer STRAT 4 Assay on the GeneXpert instrument to Assess Hormone Receptor, Ki67, and HER2 Gene Expression Status in Breast Cancer Tissue Samples

Breast cancer is the commonest cause of cancer-related mortality in African females where patients often present later and with advanced disease. Causes for delayed diagnosis include restricted diagnostic access and international controversy on interpretation of ancillary tests like immunohistochemistry (IHC). Fine needle aspirates (FNAC) are an attractive alternative although may have reduced sensitivity. The Xpert Breast Cancer STRAT4 (STRAT4) (CE-IVD*) assay (Cepheid, Sunnyvale) is a semi-quantitative reverse-transcription polymerase chain reaction assay which detects messenger RNA (mRNA) expression in breast samples for estrogen receptor (ESR1), progesterone receptor (PGR1), human epidermal growth factor receptor/Erb-B2 receptor tyrosine kinase 2 (HER2/ERBB2) and the proliferation marker, MKi67. We assessed the performance of this assay on both formalin-fixed paraffin-embedded (FFPE, n=31) and matched FNAC (n=20) samples from patients presenting with breast cancer to the Johannesburg academic hospitals. IHC and Fluorescent in situ hybridization analysis (performed on HER2-indeterminate samples) was compared with the mRNA expression of the corresponding target genes in FFPE samples, and mRNA expression on FNAC samples was compared with the FFPE results for both mRNA expression and IHC. Concordance between IHC/FISH and Xpert Breast Cancer STRAT4 in FFPE and FNAC samples using the Quick lysis (Q) method (a research-use-only modification of the validated FFPE-lysis method), showed an overall percentage agreement for ESR1 expression of 90.3% and 81.3%, and for PGR1 expression at 86.7% and 81.3% respectively in FFPE and FNAC samples. Concordance was lowest for Ki67 expression, using a binary IHC cutoff for Ki67 positivity at ≥20% staining) at 83.9% and 62.5%, for FFPE and FNAC samples, respectively. This suggests that the STRAT4 assay may be a useful ancillary test in determining HR and Ki67 status in FFPE samples and that use on FNAC samples may be feasible. Future studies should expand the sample numbers and establish locally relevant cutoffs.
Articulating Interesting Subject Positions for People with Dementia: On Hanging Out in Dutch Nursing Homes

ABSTRACT In this article, drawing on ethnographic research on everyday life and care for people with dementia in Dutch residential care, I argue that researchers who work with people with dementia can contribute to the enactment of “interesting subject positions,” thereby enriching the ways in which life with the condition is understood. The crux, I propose, is to use “hanging out” as a method and to ask “interesting questions,” an approach that enables participants to let researchers know what matters to them. Researchers, in turn, are enabled to “say more” about dementia, and to bring to light interesting subject positions.
Public acceptability change of urban road pricing schemes

Previous research has demonstrated the low public acceptability of urban road pricing schemes, in particular before being implemented. However, acceptability has changed positively in cities that have introduced road pricing. The reasons for these acceptability changes are unclear. One reason for the acceptability change after the implementation of road pricing could be people's successful reduction of their car use in line with the psychological theory of cognitive dissonance. Therefore, this study investigated public acceptability changes, private car use reductions and their relationship in response to urban road pricing. Data from the AKTA road pricing experiment in Copenhagen, Denmark was used. This dataset provides the unique possibility to link driver's acceptability change with their car use reductions. In contrast to previous studies the majority of participants in AKTA (and in Copenhagen in general) supported road pricing before the start of the field experiment. However, no change in public acceptability was observed as a consequence of the experiment. Global positioning system-based car use indicators as well as subjective reports about car use reductions show that car drivers have reduced their car use in response to road pricing. However, only limited support for a relationship between acceptability change and reductions in car use was found. The implications of these results are discussed.
ESTIMATING ACCIDENTS IN A ROAD NETWORK

This paper reviews models relating accidents to traffic flows, with particular emphasis on the appropriateness of the model form and the statistical analysis technique employed for parameter estimation. The development of new generalised linear models for predicting accidents at intersections in New Zealand is then described. It is shown that the new models fit the empirical data better than existing, simpler models. The use of the models for predicting intersection accidents in three networks is described. The paper concludes that models based on summing intersections in-flows, and estimated using ordinary (Normal) regression, are less appropriate than those based on products of conflicting flows, and estimated using Poisson or Negative Binomial regression. The latter models take better account of the mechanisms of accident occurrence, enable prediction of accident types, and provide accurate estimates of accidents in a network and the safety benefits of network flow changes. (a) For the covering entry of this conference, please see IRRD abstract no. 878228.
Implications of Cellular Mechanical Memory in Bioengineering

The ability to maintain and differentiate cells in vitro is critical to many advances in the field of bioengineering. However, on traditional, stiff (E ≈ GPa) culture substrates, cells are subjected to sustained mechanical stress that can lead to phenotypic changes. Such changes may remain even after transferring the cells to another scaffold or engrafting them in vivo and bias the outcomes of the biological investigation or clinical treatment. This persistence—or mechanical memory—was initially observed for sustained myofibroblast activation of pulmonary fibroblasts after culturing them on stiff (E ≈ 100 kPa) substrates. Aspects of mechanical memory have now been described in many in vitro contexts. In this Review, we discuss the stiffness-induced effectors of mechanical memory: structural changes in the cytoskeleton and activity of transcription factors and epigenetic modifiers. We then focus on how mechanical memory impacts cell expansion and tissue regeneration outcomes in bioengineering applications relying on prolonged 2D plastic culture, such as stem cell therapies and disease models. We propose that alternatives to traditional cell culture substrates can be used to mitigate or erase mechanical memory and improve the efficiency of downstream cell-based bioengineering applications.
Diversity matters — extending sound intensity coding by inner hair cells via heterogeneous synapses

Our sense of hearing enables the processing of stimuli that differ in sound pressure by more than six orders of magnitude. How to process a wide range of stimulus intensities with temporal precision is an enigmatic phenomenon of the auditory system. Downstream of dynamic range compression by active cochlear micromechanics, the inner hair cells (IHCs) cover the full intensity range of sound input. Yet, the firing rate in each of their postsynaptic spiral ganglion neurons (SGNs) encodes only a fraction of it. As a population, spiral ganglion neurons with their respective individual coding fractions cover the entire audible range. How such “dynamic range fractionation” arises is a topic of current research and the focus of this review. Here, we discuss mechanisms for generating the diverse functional properties of SGNs and formulate testable hypotheses. We postulate that an interplay of synaptic heterogeneity, molecularly distinct subtypes of SGNs, and efferent modulation serves the neural decomposition of sound information and thus contributes to a population code for sound intensity.
Uncommon configuration of intercostobrachial nerves, lateral roots, and absent medial cutaneous nerve of arm in a cadaveric study

The intercostobrachial nerve (ICBN) originates from the second intercostal nerve’s lateral cutaneous branch, while the median nerve (MN) typically arises from the brachial plexus’s lateral and medial roots. The medial cutaneous nerve of the arm, a branch of the medial cord of the brachial plexus, often connects with the ICBN. Variations were observed during the dissection of a 50-year-old male cadaver, including MN having two lateral roots (LR), LR1 and LR2, joining at different levels. Three ICBNs innervated the arm in this case, with the absence of the medial cutaneous nerve of the arm compensated by branches from the medial cutaneous nerve of the forearm. Understanding these anatomical variations is crucial for surgical procedures like brachioplasty, breast augmentation, axillary lymph node dissection, and orthopedic surgery. Surgeons and medical professionals must be aware of these variations to enhance preoperative planning, minimize complications, and improve patient outcomes in these procedures.
Early developmental support for preterm infants based on exploratory behaviors: A parallel randomized controlled study

Preterm infants are at high risk for developmental disabilities, and their parents are at increased risk for high stress. Early intervention programs are applied to reduce these adverse outcomes. The primary aim is to compare the efficacy of the novel Explorer Baby early intervention program for the holistic development of preterm infants. The second objective was to compare the stress levels of their mothers.
Influence of CYP2C19, CYP2D6, and ABCB1 Gene Variants and Serum Levels of Escitalopram and Aripiprazole on Treatment-Emergent Sexual Dysfunction: A Canadian Biomarker Integration Network in Depression 1 (CAN-BIND 1) Study

Objectives Treatment-emergent sexual dysfunction is frequently reported by individuals with major depressive disorder (MDD) on antidepressants, which negatively impacts treatment adherence and efficacy. We investigated the association of polymorphisms in pharmacokinetic genes encoding cytochrome-P450 drug-metabolizing enzymes, CYP2C19 and CYP2D6, and the transmembrane efflux pump, P-glycoprotein (i.e., ABCB1), on treatment-emergent changes in sexual function (SF) and sexual satisfaction (SS) in the Canadian Biomarker Integration Network in Depression 1 (CAN-BIND-1) sample. Methods A total of 178 adults with MDD received treatment with escitalopram (ESC) from weeks 0–8 (Phase I). At week 8, nonresponders were augmented with aripiprazole (ARI) (i.e., ESC + ARI, n = 91), while responders continued ESC (i.e., ESC-Only, n = 80) from weeks 8–16 (Phase II). SF and SS were evaluated using the sex effects (SexFX) scale at weeks 0, 8, and 16. We assessed the primary outcomes, SF and SS change for weeks 0–8 and 8–16, using repeated measures mixed-effects models. Results In ESC-Only, CYP2C19 intermediate metabolizer (IM) + poor metabolizers (PMs) showed treatment-related improvements in sexual arousal, a subdomain of SF, from weeks 8–16, relative to CYP2C19 normal metabolizers (NMs) who showed a decline, F(2,54) = 8.00, p < 0.001, q = 0.048. Specifically, CYP2C19 IM + PMs reported less difficulty with having and sustaining vaginal lubrication in females and erection in males, compared to NMs. Furthermore, ESC-Only females with higher concentrations of ESC metabolite, S-desmethylcitalopram (S-DCT), and S-DCT/ESC ratio in serum demonstrated more decline in SF (r = −0.42, p = 0.004, q = 0.034) and SS (r = −0.43, p = 0.003, q = 0.034), respectively, which was not observed in males. ESC-Only females also demonstrated a trend for a correlation between S-DCT and sexual arousal change in the same direction (r = −0.39, p = 0.009, q = 0.052). Conclusions CYP2C19 metabolizer phenotypes may be influencing changes in sexual arousal related to ESC monotherapy. Thus, preemptive genotyping of CYP2C19 may help to guide selection of treatment that circumvents selective serotonin reuptake inhibitor-related sexual dysfunction thereby improving outcomes for patients. Additionally, further research is warranted to clarify the role of S-DCT in the mechanisms underlying ESC-related changes in SF and SS. This CAN-BIND-1 study was registered on clinicaltrials.gov (Identifier: NCT01655706) on 27 July 2012.
Elevational range extension of the Puna Mouse, Punomys (Cricetidae), with the first record of the genus from Chile

We report an elevational record for the Andean sigmodontine Puna Mouse Punomys, which is also the first record of the genus in Chile. The record is based on a mummified specimen that we discovered at an elevation of 5,461 m (17,917 feet) in the caldera of Volcán Acamarachi, Región de Antofagasta, Chile. Results of a morphological assessment suggest that the specimen can be provisionally referred to the species P. lemminus. This new record also extends the known geographic distribution of the genus by 700 km to the south and brings the known Chilean mammal richness to a total of 170 living species and 88 genera. This finding highlights the need for increased survey efforts in more remote, high-elevation regions and demonstrates that there is still much to be learned about the mammal fauna of the Andean Altiplano. Se reporta un registro altitudinal para el roedor sigmodontino Punomys, el cual corresponde a su vez al primer hallazgo del género para Chile. Este se basa en un espécimen momificado encontrado a una elevación de 5,461 m en la caldera del Volcán Acamarachi, Región de Antofagasta, Chile. Los caracteres morfológicos sugieren que el espécimen puede ser referido provisionalmente a la especie P. lemminus. Este nuevo registro amplía la distribución geográfica conocida del género en 700 km al sur, y eleva la riqueza de mamíferos vivientes chilenos a un nuevo total de 170 especies y 88 géneros. Este hallazgo resalta la necesidad de aumentar los esfuerzos de prospección en las regiones más remotas y de mayor altitud y demuestra que aún queda mucho por aprender sobre el ensamble de los mamíferos del Altiplano andino.
Practical measurement system for determination of refractive index and thickness using low-coherence interferometry

Very recently, we developed a computer-controlled low- coherence interferometer system with precise translation stages for simultaneous measurement of refractive index and thickness. Both phase and group indices can be determined automatically in a wide thickness range of 20 micrometer to a few mm. This paper presents the system configuration and the measurement principle accompanied with typical examples of automatic measurement.
Complex early rifting in Valles Marineris: Results from preliminary geologic mapping of the Ophir Planum Region of Mars

Photogeologic mapping of the Ophir Planum quadrangle was undertaken to solve two main problems: (1) what controlled the location, orientation, and growth of Ophir Planum grabens; and (2) how are the grabens and trough faulting related. The rich geological history of the Ophir Planum quadrangle underscores the fundamental importance of faulting in the early growth of Valles Marineris.
Botulinum Toxin for the Management of Pelvic Floor Tension Myalgia and Persistent Pelvic Pain

Meta-analyses of randomized data do not support the use of botulinum toxin for the treatment of pelvic floor tension myalgia and persistent pelvic pain. OBJECTIVE: To systematically review the literature on use of botulinum toxin to treat pelvic floor tension myalgia and persistent pelvic pain. DATA SOURCES: The ClinicalTrials.gov, PubMed, EMBASE, and Scopus databases were searched from inception to November 2022 by two independent assessors (B.L.K. and F.G.L.). Identified studies were screened by title and abstract and included after full-text review. Data extraction was subsequently performed and recorded in Microsoft Excel. METHODS: This study was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines after registration in PROSPERO (CRD42022289132). All randomized studies, prospective studies with more than five participants, and retrospective studies with more than 10 participants published in English or French and assessing the use of botulinum toxin for the treatment of pelvic floor tension myalgia and persistent pelvic pain in women were included. Meta-analyses were performed on randomized data. TABULATION, INTEGRATION, AND RESULTS: Of 4,722 articles identified, 24 satisfied inclusion criteria. A meta-analysis of five randomized controlled trials totaling 329 participants demonstrated no differences in patient- and clinician-reported outcome measures, including pain, dyspareunia, sexual function, and vaginal manometry. Mean duration of follow-up was 6 months. A qualitative analysis of 14 prospective and four retrospective studies including 804 participants is supportive of botulinum toxin; however, the quality of data is low, and there is marked heterogeneity between studies. CONCLUSION: Meta-analyses of randomized data do not support the use of botulinum toxin to treat pelvic floor tension myalgia and persistent pelvic pain. Failure of these data to confirm the findings of nonrandomized prospective studies that suggest a treatment benefit may be attributable to the absence of placebo control and confounding outcomes obtained from an active comparator group. Further randomized controlled trials with true placebo are strongly recommended. SYSTEMATIC REVIEW REGISTRATION: PROSPERO, CRD42022289132.
Complete genome sequences of Ruminococcus torques strains JCM 36208 and JCM 36209, isolated from the feces of a healthy Japanese male

ABSTRACT Here, we report the complete genome sequences of two Ruminococcus torques strains (JCM 36208 and JCM 36209) that were newly isolated from the feces of a healthy Japanese male. Both genomes consist of a single circular chromosome with a length of ~2.8 Mbp and a G+C content of 41.8%.