Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated model discovery for muscle using constitutive recurrent neural networks

The stiffness of soft biological tissues not only depends on the applied deformation, but also on the deformation rate. To model this type of behavior, traditional approaches select a specific time-dependent constitutive model and fit its parameters to experimental data. Instead, a new trend now suggests a machine-learning based approach that simultaneously discovers both the best model and best parameters to explain given data. Recent studies have shown that feed-forward constitutive neural networks can robustly discover constitutive models and parameters for hyperelastic materials. However, feed-forward architectures fail to capture the history dependence of viscoelastic soft tissues. Here we combine a feed-forward constitutive neural network for the hyperelastic response and a recurrent neural network for the viscous response inspired by the theory of quasi-linear viscoelasticity. Our novel rheologically-informed network architecture discovers the time-independent initial stress using the feed-forward network and the time-dependent relaxation using the recurrent network. We train and test our combined network using unconfined compression relaxation experiments of passive skeletal muscle and compare our discovered model to a neo Hookean standard linear solid and to a vanilla recurrent neural network with no mechanics knowledge. We demonstrate that, for limited experimental data, our new constitutive recurrent neural network discovers models and parameters that satisfy basic physical principles and generalize well to unseen data. We discover a Mooney-Rivlin type two-term initial stored energy function that is linear in the first invariant I1 and quadratic in the second invariant I2 with stiffness parameters of 0.60kPa and 0.55kPa. We also discover a Prony-series type relaxation function with time constants of 0.362s, 2.54s, and 52.0s with coefficients of 0.89, 0.05, and 0.03. Our newly discovered model outperforms both the neo Hookean standard linear solid and the vanilla recurrent neural network in terms of prediction accuracy on unseen data. Our results suggest that constitutive recurrent neural networks can autonomously discover both model and parameters that best explain experimental data of soft viscoelastic tissues. Our source code, data, and examples are available at https://github.com/LivingMatterLab.
Antithetical contribution of primary and non-primary auditory cortex while listening to speech in noisy scenes

Invasive and non-invasive electrophysiological measurements during “cocktail-party”-like listening indicate that neural activity in the human auditory cortex (AC) “tracks” the envelope of relevant speech. Due to the measurements’ limited coverage and/or spatial resolution, however, the distinct contribution of primary and non-primary auditory areas remains unclear. Using 7-Tesla fMRI, here we measured brain responses of participants attending to one speaker, without and with another concurrent speaker. Using voxel-wise modeling, we observed significant speech envelope tracking in bilateral Heschl’s gyrus (HG) and right middle superior temporal sulcus (mSTS), despite the sluggish fMRI responses and slow temporal sampling. Neural activity was either positively (HG) or negatively (mSTS) correlated to the speech envelope. Further analyses comparing the similarity between spatial response patterns in the concurrent speakers and single speaker conditions indicated that whereas tracking in HG reflected both relevant and (to a lesser extent) non-relevant speech, right mSTS selectively represented the relevant speech signal. Additionally, in right mSTS, the similarity strength correlated with the participant’s comprehension of relevant speech. These results indicate that primary and non-primary AC antithetically process ongoing speech suggesting a push-pull of acoustic and linguistic information.
A spatial code for temporal cues is necessary for sensory learning

The temporal structure of sensory inputs contains essential information for their interpretation by the brain1–9. Sensory systems represent these temporal cues through two codes: the temporal sequences of neuronal activity and the spatial patterns of neuronal firing rate3,7,10–20. However, it is still unknown which of these two coexisting codes causally drives sensory decisions3,10,20,21. To separate their contributions, we designed an optogenetic stimulation paradigm in the mouse auditory cortex to generate neuronal activity patterns differing exclusively along their temporal or spatial dimensions. Training mice to discriminate these patterns shows that they efficiently learn to discriminate spatial but not temporal patterns, indicating that spatial representations are necessary for sensory learning. In line with this result, we observed, based on large-scale neuronal recordings of the auditory system, that the auditory cortex is the first region in which spatial patterns efficiently represent temporal auditory cues varying over several hundred milliseconds. This feature is shared by the deep layers of neural networks trained to categorise time-varying sounds. Therefore, the emergence of a spatial code for temporal sensory cues is a necessary condition to associate temporally structured stimuli to decisions. We expect this constraint to be crucial for re-engineering perception by cortical stimulation.
Interactions between fluid and fibers in a turbulent backward-facing step flow

In this work, a turbulent backward-facing step flow at Reynolds number ReH = 17 520, laden with rod-like particles, is investigated by means of particle image velocimetry. Particle loadings tested are within 0.02% and 0.05% volume fractions; thus, the suspensions may be considered as dilute. The high spatial resolution allows the identification of fiber orientation within the flow, so that mutual interactions between phases can be investigated by considering flow modifications and phenomena related to preferential concentration and orientation of fibers. Fibers’ concentration data show a moderate trend to accumulate at the channel centreline, whereas orientation data display a strong preferential orientation of fibers. Specifically, the local fibers’ orientation is correlated to the flow field in terms of mean flow direction and plane of maximum shear. The occurrence of a symmetrical orientation profile with respect to the channel centre-line is reported as well as the tendency to recover such profile downstream of the step.
Mindfulness meditation and bimanual coordination control: study of acute effects and the mediating role of cognition

Introduction Mindfulness meditation (MM) involves and benefits cognitive functioning, especially attention and inhibition processes, which are also implicated in the control of complex motor skills, such as bimanual coordination. Thus, MM practice could potentially enhance bimanual coordination control through its cognitive benefits. Accordingly, in this study, we investigated the acute effects of a brief MM session on bimanual coordination dynamics, attention, and inhibition abilities, as well as the mediation link between MM’s cognitive and motor improvements. Methods Healthy meditation-naïve (novices, n = 29) and meditation-experienced participants (meditators, n = 26) were randomly assigned to either an active control intervention (attentive listening to a documentary podcast) or a MM intervention (breathing and open monitoring exercise), both lasting 15 min. In the motor domain, pre- and post-tests assessed participants’ ability to intentionally maintain the anti-phase coordination pattern at maximal movement frequency and resist the spontaneous transition to the in-phase pattern. In the cognitive domain, the participants’ attentional, perceptual inhibition and motor inhibition abilities were assessed. Results Following both interventions, meditators and novices improved the stability of their anti-phase coordination pattern (p = 0.034, ηp2 = 0.10) and their attentional performance (p’s < 0.001, ηp2 > 0.40). Only following the MM intervention, meditators and novices improved their ability to intentionally maintain the anti-phase pattern by delaying or even suppressing the spontaneous transition to in-phase (p’s < 0.05, ηp2 ≥ 0.11), and improved concomitantly their motor inhibition scores (p = 0.011, ηp2 = 0.13). No effects were found on perceptual inhibition. The increase in motor inhibition capacities did not however statistically mediate the observed acute effects of MM on bimanual coordination control. Conclusion We showed that a single MM session may have acute benefits in the motor domain regardless of the familiarity with MM practice. Although these benefits were concomitant to enhanced attentional and motor inhibition abilities, no formal mediation link could be established between the observed motor and cognitive benefits. This study paves the way for the investigation of the mechanisms underlying MM effects on motor control, as well as longer-term benefits.
Crustal structure of the Ethiopian Northwestern Plateau and central Afar from receiver function analysis

In magma-rich continental rifts extension by magma intrusion is thought to accommodate much of the extension. We aim to constrain major melt reservoirs in the crust during magma-rich rifting by applying P-to-S receiver functions (RFs) using legacy teleseismic data having magnitudes Mb > 6.0 and epicentral distances ranging from 30° to 90° and collected between the years 2000 and 2013 in 17 temporary broadband stations in Ethiopia and Eritrea. The majority of the NW Plateau crust shows fast Vs of ∼4–4.7 km/s with localized slow Vs (3.2 km/s) and high Vp/Vs (1.85–2.0) in the mid-crust (∼10–25 km depth). The seismic velocity beneath the Afar crust is fairly homogeneous except beneath the current locus of strain at the magmatic segments, which have a relatively fast Vs. (∼4.5 km/s) at a shallow (∼6–14 km) depth underlain by slower Vs. (<3.2 km/s) and high Vp/Vs (2.0) at lower crustal depths (∼20–25 km). The Moho is sharp beneath most of the plateau stations and more gradational beneath Afar with estimated values of 36–44 km in the NW plateau and 26–30 km in Afar. The results point towards the presence of partial melt in localized places in the mid-crust beneath the NW plateau, and in the lower crust beneath the west of Afar, and particularly focused in the lower crust beneath the magmatic segments in Afar. The results suggest that the lower crust is an important melt reservoir for rift-related magmatic processes. The presence of melt in the NW plateau crust is more difficult to explain but is potentially linked to the broad extension of the plateau, or lateral migration of melt from the rift.
Serum immune mediators as novel predictors of response to anti-PD-1/PD-L1 therapy in non-small cell lung cancer patients with high tissue-PD-L1 expression

Background Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related morbidity and mortality worldwide. Immune checkpoint inhibitors (ICIs) including anti-PD-1 and anti-PD-L1 antibodies, have significantly changed the treatment outcomes with better overall survival, but only 15-40% of the patients respond to ICIs therapy. The search for predictive biomarkers of responses is warranted for better clinical outcomes. We aim here to identify pre-treatment soluble immune molecules as surrogate biomarkers for tissue PD-L1 (TPD-L1) status and as predictors of response to anti-PD-1/PD-L1 therapy in NSCLC patients. Sera from 31 metastatic NSCLC patients, eligible for anti-PD-1/PD-L1 or combined chemoimmunotherapy, were collected prior to treatment. Analysis of soluble biomarkers with TPD-L1 status showed significant up/down regulation of the immune inhibitory checkpoint markers (sSiglec7, sSiglec9, sULBP4 and sPD-L2) in patients with higher TPD-L1 (TPD-L1 >50%) expression. Moreover, correlation analysis showed significant positive linear correlation of soluble PD-L1 (sPD-L1) with higher TPD-L1 expression. Interestingly, only responders in the TPD-L1 >50% group showed significant down regulation of the immune inhibitory markers (sPD-L2, sTIMD4, sNectin2 and CEA). When responders vs. non-responders were compared, significant down regulation of other immune inhibitory biomarkers (sCD80, sTIMD4 and CEA) was recorded only in responding patients. In this, the optimal cut-off values of CD80 <91.7 pg/ml and CEA <1614 pg/ml were found to be significantly associated with better progression free survival (PFS). Indeed, multivariate analysis identified the cutoff-value of CEA <1614 pg/ml as an independent predictor of response in our patients. We identified here novel immune inhibitory/stimulatory soluble mediators as potential surrogate/predictive biomarkers for TPD-L1 status, treatment response and PFS in NSCLC patients treated with anti-PD-1/PD-L1 therapy.
The detailed classification of the interlobar artery and the artery crossing intersegmental planes in the right upper lobe

Background With the prevalence of three-dimensional computed tomography bronchography and angiography (3D-CTBA) and the development of anatomical segmentectomy, several studies have analyzed the branching patterns of peripheral segmental arteries in the right upper lobe (RUL). Nevertheless, the detailed classification of the branching patterns of the interlobar artery and the artery crossing intersegmental planes remains unknown. Thus, we conducted a retrospective study to analyze the variations of the interlobar artery and the artery crossing intersegmental planes in the RUL using 3D-CTBA. Materials and methods A total of 600 patients with ground-glass opacity (GGO) who had undergone 3D-CTBA preoperatively at Hebei General Hospital between September 2020 and September 2022 were used for the retrospective study. We reviewed the anatomical variations of the RUL arteries in these patients using 3D-CTBA images. Results The branching patterns of the RUL artery were classified into the following four categories: trunk superior (Tr. sup), Tr. sup + interlobar artery, Tr. sup + trunk inferior (Tr. inf), and Tr. sup + Tr. inf + interlobar artery. The branching patterns of the interlobar artery were subclassified into four subtypes: posterior ascending artery (A. pos), anterior ascending artery (A. ant), A. pos + A. ant, and ascending artery (A. asc). The artery crossing intersegmental planes contains two types: type A, anterior subsegmental artery crossing intersegmental planes (AX1b); type B, recurrent artery crossing intersegmental planes (AX. rec). Conclusion The variation types of blood vessels in the RUL are complex. This study explored the detailed classification of the interlobar artery and the artery crossing intersegmental planes. It can help thoracic surgeons understand the anatomy variations, accurately locate lesions before surgery, and effectively plan surgeries.
Post-operative pulmonary complications after thoracic and upper abdominal procedures at referral hospitals in Amhara region, Ethiopia: a multi-center study

Background Thoraco-abdominal surgery cuts through muscle, disrupting the normal structure and function of the respiratory muscles, resulting in lower lung volumes and a higher risk of developing post-operative pulmonary complications (PPC). PPC remains an important cause of post-operative morbidity and mortality and impacts the long-term outcomes of patients after hospital discharge. This study was aimed at determining the incidence and factors associated with postoperative pulmonary complications among patients who underwent thoracic and upper abdominal surgery in the Amhara region of Ethiopia. Methods A multi-center follow-up study was conducted from April 1, 2022, to June 30, 2022, at comprehensive specialized hospitals in Amhara regional state, northwest Ethiopia. 424 patients were consecutively included in this study, with a response rate of 100%. A chart review and patient interview were used to collect data. A logistic regression analysis was performed to assess the strength of the association of independent variables with postoperative pulmonary complications.The crude odds ratio (COR) and adjusted odds ratio (AOR) with the corresponding 95% confidence interval were computed. Variables with a p-value of <0.05 were considered statistically significant predictors of the outcome variable. Results The incidence of postoperative pulmonary complication was 24.5%. Emergency procedures, preoperative SpO2 < 94%, duration of surgery >2 h, patients with a nasogastric tube, intraoperative blood loss >500 ml and post-operative albumin <3.5 g/dl were factors associated with pulmonary complications. The most common complications were pneumonia (9.9%) followed by respiratory infection (4.2%). Conclusion The incidence of postoperative pulmonary complication after thoracic and upper abdominal surgery remains high. Preoperative SpO2, duration of surgery, patients having a nasogastric tube, intraoperative blood loss and post-operative albumin were factors associated with post-operative pulmonary complications.
Leveraging the placenta to advance neonatal care

The impact of placental dysfunction and placental injury on the fetus and newborn infant has become a topic of growing interest in neonatal disease research. However, the use of placental pathology in directing or influencing neonatal clinical management continues to be limited for a wide range of reasons, some of which are historical and thus easily overcome today. In this review, we summarize the most recent literature linking placental function to neonatal outcomes, focusing on clinical placental pathology findings and the most common neonatal diagnoses that have been associated with placental dysfunction. We discuss how recent technological advances in neonatal and perinatal medicine may allow us to make a paradigm shift, in which valuable information provided by the placenta could be used to guide neonatal management more effectively, and to ultimately enhance neonatal care in order to improve our patient outcomes. We propose new avenues of clinical management in which the placenta could serve as a diagnostic tool toward more personalized neonatal intensive care unit management.
Grain yield and quality performances of different late-season rice cultivars in response to experimental warming in subtropical China

Introduction Climate warming has pronounced effects on rice production in China. However, late-seasons rice cultivars are diverse in double rice cropping systems, and the actual responses in grain yield and quality of different late-season rice cultivars to climate warming are still unclear. Methods A two-year field warming experiment was conducted by using free-air temperature increase facilities with three widely-planted late-season rice cultivars, including Taiyou398 (TY, short growth duration indica hybrid rice), Jiuxiangnian (JXN, long growth duration indica inbred rice), and Yongyou1538 (YY, long growth duration indica-japonica hybrid rice) in a double rice cropping system in subtropical China. Results Warming (1.9–2.0°C) had no significant effects on the grain yields of TY and JXN, but significantly decreased that of YY by 4.8% relative to ambient treatment due to a reduction of spikelet number. Compared to ambient treatment, the head rice yields of TY and YY did not change while that of JXN increased by 6.3% under warming conditions. Warming significantly increased the head rice rates of JXN and YY by 6.6% and 7.8%, and the chalky grain rates of TY, JXN, and YY by 79.1%, 21.6%, and 7.6%, respectively. Under warming conditions, the amylose content of JXN and YY decreased significantly by 7.5% and 8.8%, and the setback of three cultivars decreased significantly by an average of 41.5%. Conclusion Warming could improve the milling and eating qualities of long growth duration late-season rice (JXN and YY) and increase or maintain their head rice yield, even though decreased the grain yield of indica-japonica hybrid rice (YY). These results will provide a better understanding for the selection of suitable late-season rice cultivars under future climate warming conditions.
Genetic analysis and QTL mapping of domestication-related traits in chili pepper (Capsicum annuum L.)

Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.
Broad-spectrum anti-HIV activity and high drug resistance barrier of lipopeptide HIV fusion inhibitor LP-19

Lipopeptide-19, a HIV fusion inhibitor (LP-19), has showed potent anti-HIV activity. However, there is still limited information of the antiviral activity against different subtype clinical isolates and the drug resistance barrier of LP-19. Therefore, 47 HIV clinical isolates were selected for this study. The viral features were identified, in which 43 strains are CCR5 tropisms, and 4 strains are CCR5/CXCR4 tropisms, and there are 6 subtype B’, 15 CRF01_AE, 14 CRF07_BC, 2 CRF08_BC and 10 URF strains. These 47 viruses were used to detected and analyze the inhibitory activities of LP-19. The results showed that the average 50% inhibitory concentration (IC50) and 90% inhibitory concentration (IC90) of LP-19 were 0.50 nM and 1.88 nM, respectively. The average IC50 of LP-19 to B’, CRF01_AE, CRF07_BC, CRF08_BC, and URF strains was 0.76 nM, 0.29 nM, 0.38 nM, 0.85 nM, and 0.44 nM, respectively. C34 and Enfuvirtide (T-20), two fusion inhibitors, were compared on the corresponding strains simultaneously. The antiviral activity of LP-19 was 16.7-fold and 86-fold higher than that of C34 and T-20. The antiviral activity of LP-19, C34, and T-20 were further detected and showed IC50 was 0.15 nM, 1.02 nM, and 66.19 nM, respectively. IC50 of LP-19 was about 7-fold and 441-fold higher compared to C34 and T-20 against HIV-1 NL4-3 strains. NL4-3 strains were exposed to increasing concentrations of LP-19 and C34 in MT-2 cell culture. The culture virus was sequenced and analyzed. The results showed that A243V mutation site identified at weeks 28, 32, 38, and 39 of the cell culture in the gp41 CP (cytoplasmic domain) region. NL4-3/A243V viruses containing A243V mutation were constructed. Comparing the antiviral activities of LP-19 against HIV NL4-3 to HIV strains (only 1.3-fold), HIV did not show drug resistance when LP-19 reached 512-fold of the initial concentration under the drug pressure for 39 weeks. This study suggests that LP-19 has broad-spectrum anti-HIV activity, and high drug resistance barrier.