Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression Elements Derived From Plant Sequences Provide Effective Gene Expression Regulation and New Opportunities for Plant Biotechnology Traits

Plant biotechnology traits provide a means to increase crop yields, manage weeds and pests, and sustainably contribute to addressing the needs of a growing population. One of the key challenges in developing new traits for plant biotechnology is the availability of expression elements for efficacious and predictable transgene regulation. Recent advances in genomics, transcriptomics, and computational tools have enabled the generation of new expression elements in a variety of model organisms. In this study, new expression element sequences were computationally generated for use in crops, starting from native Arabidopsis and maize sequences. These elements include promoters, 5′ untranslated regions (5′ UTRs), introns, and 3′ UTRs. The expression elements were demonstrated to drive effective transgene expression in stably transformed soybean plants across multiple tissues types and developmental stages. The expressed transcripts were characterized to demonstrate the molecular function of these expression elements. The data show that the promoters precisely initiate transcripts, the introns are effectively spliced, and the 3′ UTRs enable predictable processing of transcript 3′ ends. Overall, our results indicate that these new expression elements can recapitulate key functional properties of natural sequences and provide opportunities for optimizing the expression of genes in future plant biotechnology traits.
Polarization Label-Free Microscopy Imaging of Biological Samples by Exploiting the Zeeman Laser Emission

Mueller Matrix Microscopy exploits the generation and the analysis of polarized light to create label-free contrast in biological images. However, when dealing with Optical Scanning Microscopy, it is required a fast generation of the polarization states in order to obtain a good Signal-to-Noise Ratio at the pixel-dwell time rate. In this work, we propose a microscopy system based on a scanning beam architecture that is exploiting the simultaneous emission of orthogonal polarization states from a Zeeman laser to provide Mueller Matrix images. This approach is based on the detection of an interference signal that allows to time-encode polarization states directly from the laser source, without the need for further active components for the management of the polarization states. We provide the theoretical model behind this approach and we apply our new method to the imaging of biological samples. Our Mueller Matrix imaging setup enables high-speed scanning microscopy, while preserving compactness and simplicity of construction. Our findings may lead to more effective dissemination of label-free techniques and their use by biological researchers.
Socio-Technical Changes for Sustainable Rice Production: Rice Husk Amendment, Conservation Irrigation, and System Changes

Rice is a staple food and primary source of calories for much of the world. However, rice can be a dietary source of toxic metal(loid)s to humans, and its cultivation creates atmospheric greenhouse gas emissions and requires high water use. Because rice production consumes a significant amount of natural resources and is a large part of the global agricultural economy, increasing its sustainability could have substantial societal benefits. There are opportunities for more sustainable field production through a combination of silicon (Si) management and conservation irrigation practices. As a Si-rich soil amendment, rice husks can limit arsenic and cadmium uptake, while also providing plant vigor in drier soil conditions. Thus, husk addition and conservation irrigation may be more effective to attenuate the accumulation of toxic metal(loid)s, manage water usage and lower climate impacts when implemented together than when either is implemented separately. This modified field production system would take advantage of rice husks, which are an underutilized by-product of milled rice that is widely available near rice farm sites, and have ~10% Si content. Husk application could, alongside alternate wetting and drying or furrow irrigation management, help resolve multiple sustainability challenges in rice production: (1) limit arsenic and cadmium accumulation in rice; (2) minimize greenhouse gas emissions from rice production; (3) decrease irrigation water use; (4) improve nutrient use efficiency; (5) utilize a waste product of rice processing; and (6) maintain plant-accessible soil Si levels. This review presents the scientific basis for a shift in rice production practices and considers complementary rice breeding efforts. It then examines socio-technical considerations for how such a shift in production practices could be implemented by farmers and millers together and may bring rice production closer to a bio-circular economy. This paper's purpose is to advocate for a changed rice production method for consideration by community stakeholders, including producers, millers, breeders, extension specialists, supply chain organizations, and consumers, while highlighting remaining research and implementation questions.
Mosmo Is Required for Zebrafish Craniofacial Formation

Hedgehog (Hh) signaling is a highly regulated molecular pathway implicated in many developmental and homeostatic events. Mutations in genes encoding primary components or regulators of the pathway cause an array of congenital malformations or postnatal pathologies, the extent of which is not yet fully defined. Mosmo (Modulator of Smoothened) is a modulator of the Hh pathway, which encodes a membrane tetraspan protein. Studies in cell lines have shown that Mosmo promotes the internalization and degradation of the Hh signaling transducer Smoothened (Smo), thereby down-modulating pathway activation. Whether this modulation is essential for vertebrate embryonic development remains poorly explored. Here, we have addressed this question and show that in zebrafish embryos, the two mosmo paralogs, mosmoa and mosmob, are expressed in the head mesenchyme and along the entire ventral neural tube. At the cellular level, Mosmoa localizes at the plasma membrane, cytoplasmic vesicles and primary cilium in both zebrafish and chick embryos. CRISPR/Cas9 mediated inactivation of both mosmoa and mosmob in zebrafish causes frontonasal hypoplasia and craniofacial skeleton defects, which become evident in the adult fish. We thus suggest that MOSMO is a candidate to explain uncharacterized forms of human congenital craniofacial malformations, such as those present in the 16p12.1 chromosomal deletion syndrome encompassing the MOSMO locus.
Changes in the Antioxidant and Mineral Status of Rabbits After Administration of Dietary Zinc and/or Thyme Extract

This study was aimed at determining the impact of organic zinc (Zn) and thyme extract (TE) administration, given alone or together for 6 weeks, on the antioxidant and mineral status (Zn, Cu, Fe, and Mn) in the plasma and tissues of growing rabbits. A total of 96 rabbits of age 35 days were randomly assigned to one of four treatment groups: a control group (C), a Zn group supplemented with dietary zinc (50 mg/kg), a TE group receiving thyme extract applied in drinking water (1 ml/L), and a Zn + TE group treated with both additives. Lipid peroxidation in the plasma was influenced by Zn intake and in the kidney was affected by both the Zn and TE treatment (P < 0.05). Zn supplementation led to a significant increase in glutathione peroxidase activity (P = 0.017), total antioxidant capacity (P = 0.009) and total thiol groups level (P = 0.047) in the kidney, with the highest values occurring in rabbits receiving the combination Zn + TE. Administration of TE influenced Zn content in the kidney (P < 0.001), while zinc intake decreased Cu concentration in muscle (P = 0.021). In conclusion, the simultaneous administration of organic Zn and TE positively affected the antioxidant response of kidneys and can be used for improving the antioxidant status of growing rabbits.
Wearable Robots: An Original Mechatronic Design of a Hand Exoskeleton for Assistive and Rehabilitative Purposes

Robotic devices are being employed in more and more sectors to enhance, streamline, and augment the outcomes of a wide variety of human activities. Wearable robots arise indeed as of-vital-importance tools for telerehabilitation or home assistance targeting people affected by motor disabilities. In particular, the field of “Robotics for Medicine and Healthcare” is attracting growing interest. The development of such devices is a primarily addressed topic since the increasing number of people in need of rehabilitation or assistive therapies (due to population aging) growingly weighs on the healthcare systems of the nation. Besides, the necessity to move to clinics represents an additional logistic burden for patients and their families. Among the various body parts, the hand is specially investigated since it most ensures the independence of an individual, and thus, the restoration of its dexterity is considered a high priority. In this study, the authors present the development of a fully wearable, portable, and tailor-made hand exoskeleton designed for both home assistance and telerehabilitation. Its purpose is either to assist patients during activities of daily living by running a real-time intention detection algorithm or to be used for remotely supervised or unsupervised rehabilitation sessions by performing exercises preset by therapists. Throughout the mechatronic design process, special attention has been paid to the complete wearability and comfort of the system to produce a user-friendly device capable of assisting people in their daily life or enabling recorded home rehabilitation sessions allowing the therapist to monitor the state evolution of the patient. Such a hand exoskeleton system has been designed, manufactured, and preliminarily tested on a subject affected by spinal muscular atrophy, and some results are reported at the end of the article.
Performance of Three Asthma Predictive Tools in a Cohort of Infants Hospitalized With Severe Bronchiolitis

Childhood asthma develops in 30–40% of children with severe bronchiolitis but accurate prediction remains challenging. In a severe bronchiolitis cohort, we applied the Asthma Predictive Index (API), the modified Asthma Predictive Index (mAPI), and the Pediatric Asthma Risk Score (PARS) to predict asthma at age 5 years. We applied the API, mAPI, and PARS to the 17-center cohort of infants hospitalized with severe bronchiolitis during 2011–2014 (35th Multicenter Airway Research Collaboration, MARC-35). We used data from the first 3 years of life including parent interviews, chart review, and specific IgE testing to predict asthma at age 5 years, defined as parent report of clinician-diagnosed asthma. Among 875/921 (95%) children with outcome data, parent-reported asthma was 294/875 (34%). In MARC-35, a positive index/score for stringent and loose API, mAPI, and PARS were 24, 68, 6, and 55%, respectively. The prediction tools' AUCs (95%CI) ranged from 0.57 (95%CI 0.54–0.59) to 0.68 (95%CI 0.65–0.71). The positive likelihood ratios were lower in MARC-35 compared to the published results from the original cohorts. In this high-risk population of infants hospitalized with severe bronchiolitis, API, mAPI, and PARS had sub-optimal performance (AUC <0.8). Highly accurate (AUC >0.8) asthma prediction tools are desired in infants hospitalized with severe bronchiolitis.
Advances and Prospects in Biomaterials for Intervertebral Disk Regeneration

Low-back and neck-shoulder pains caused by intervertebral disk degeneration are highly prevalent among middle-aged and elderly people globally. The main therapy method for intervertebral disk degeneration is surgical intervention, including interbody fusion, disk replacement, and diskectomy. However, the stress changes caused by traditional fusion surgery are prone to degeneration of adjacent segments, while non-fusion surgery has problems, such as ossification of artificial intervertebral disks. To overcome these drawbacks, biomaterials that could endogenously regenerate the intervertebral disk and restore the biomechanical function of the intervertebral disk is imperative. Intervertebral disk is a fibrocartilaginous tissue, primarily comprising nucleus pulposus and annulus fibrosus. Nucleus pulposus (NP) contains high water and proteoglycan, and its main function is absorbing compressive forces and dispersing loads from physical activities to other body parts. Annulus fibrosus (AF) is a multilamellar structure that encloses the NP, comprises water and collagen, and supports compressive and shear stress during complex motion. Therefore, different biomaterials and tissue engineering strategies are required for the functional recovery of NP and AF based on their structures and function. Recently, great progress has been achieved on biomaterials for NP and AF made of functional polymers, such as chitosan, collagen, polylactic acid, and polycaprolactone. However, scaffolds regenerating intervertebral disk remain unexplored. Hence, several tissue engineering strategies based on cell transplantation and growth factors have been extensively researched. In this review, we summarized the functional polymers and tissue engineering strategies of NP and AF to endogenously regenerate degenerative intervertebral disk. The perspective and challenges of tissue engineering strategies using functional polymers, cell transplantation, and growth factor for generating degenerative intervertebral disks were also discussed.
Bacterial Communities Present Distinct Co-occurrence Networks in Sediment and Water of the Thermokarst Lakes in the Yellow River Source Area

Thermokarst lakes are a ubiquitous and important landscape feature in cold regions and are changing tremendously due to the accelerated climate change. In thermokarst lakes, sediment and water are two distinct but highly interconnected habitats, harboring different bacterial communities in terms of taxonomic composition. However, the co-occurrence networks of these bacterial communities remain unclear. Here, we investigate the co-occurrence ecological networks of sediment and water bacterial communities for thermokarst lakes in the Yellow River Source Area on the Qinghai-Tibet Plateau. The results show that the bacterial communities construct distinct co-occurrence networks in sediment and water. The metacommunity network was parsed into four major modules formed by the operational taxonomic units (OTUs) enriched in sediment or water independently, and water-enriched OTUs exhibited much closer interconnections than sediment-enriched OTUs. When considering the sediment and water bacterial networks separately, different topological properties and modular patterns present: the sediment bacterial network was more clustered while the modules less responded to the environmental variables. On the contrary, the water bacterial network was more complex with the OTUs more interconnected and its modules more responded to the environmental variables. Moreover, the results of the structural equation model suggest that, by the influence of environmental variations on individual modules, the water bacterial communities would be more vulnerable under the fact of accelerating climate change. This study provides insights beyond a conventional taxonomic perspective, adding our knowledge of the potential mechanisms structuring bacterial community assembly and improving our prediction of the responses of this fast-changing ecosystem to future climate change.
The Effects of Intermittent Theta Burst Stimulation on Functional Brain Network Following Stroke: An Electroencephalography Study

Objective: Intermittent theta burst stimulation (iTBS) is a special form of repetitive transcranial magnetic stimulation (rTMS), which effectively increases cortical excitability and has been widely used as a neural modulation approach in stroke rehabilitation. As effects of iTBS are typically investigated by motor evoked potentials, how iTBS influences functional brain network following stroke remains unclear. Resting-state electroencephalography (EEG) has been suggested to be a sensitive measure for evaluating effects of rTMS on brain functional activity and network. Here, we used resting-state EEG to investigate the effects of iTBS on functional brain network in stroke survivors. Methods: We studied thirty stroke survivors (age: 63.1 ± 12.1 years; chronicity: 4.0 ± 3.8 months; UE FMA: 26.6 ± 19.4/66) with upper limb motor dysfunction. Stroke survivors were randomly divided into two groups receiving either Active or Sham iTBS over the ipsilesional primary motor cortex. Resting-state EEG was recorded at baseline and immediately after iTBS to assess the effects of iTBS on functional brain network. Results: Delta and theta bands interhemispheric functional connectivity were significantly increased after Active iTBS (P = 0.038 and 0.011, respectively), but were not significantly changed after Sham iTBS (P = 0.327 and 0.342, respectively). Delta and beta bands global efficiency were also significantly increased after Active iTBS (P = 0.013 and 0.0003, respectively), but not after Sham iTBS (P = 0.586 and 0.954, respectively). Conclusion: This is the first study that used EEG to investigate the acute neuroplastic changes after iTBS following stroke. Our findings for the first time provide evidence that iTBS modulates brain network functioning in stroke survivors. Acute increase in interhemispheric functional connectivity and global efficiency after iTBS suggest that iTBS has the potential to normalize brain network functioning following stroke, which can be utilized in stroke rehabilitation.
Acute Stroke With Large Vessel Occlusion and Minor Clinical Deficits: Prognostic Factors and Therapeutic Implications

Background and Purpose: The optimal acute management of patients with large vessel occlusion (LVO) and minor clinical deficits on admission [National Institutes of Health Stroke Scale (NIHSS) ≤ 4] remains to be elucidated. The aim of the present study was to investigate the prognostic factors and therapeutic management of those patients. Methods: In this retrospective cohort study, we investigated (1) all patients with acute ischemic stroke due to an LVO who underwent mechanical thrombectomy (MT) and (2) all patients with minor clinical deficits (NIHSS ≤ 4) on admission due to an LVO between January 2013 and December 2016 at the University Medical Center Erlangen. We dichotomized management of patients with minor deficits treated with MT for analysis according to immediate mechanical thrombectomy (IT) and initial medical management with rescue intervention (MM) in case of secondary deterioration. Primary endpoints were secondary deterioration, in-hospital mortality, and functional outcome on day 90 (dichotomized modified Rankin Scale 0–2: favorable, 3–6: poor). Results: Two hundred twenty-three patients (83% with anterior circulation stroke, 13 (6%) with minor deficits) treated with MT and 88 patients with minor deficits due to LVO [13 (15%) treated with MT] were included. Secondary deterioration (n = 19) was independently associated with poor outcome in patients with minor deficits and LVO [odds ratio (OR), 0.060; 95% confidence interval (CI), 0.013–0.280], which in turn was associated with the occlusion site [especially M1 occlusion: 11 (58%) vs. 3 (4%) in patients without secondary deterioration, p < 0.0001]. IT (n = 8) was associated with a lower intrahospital mortality compared to MM (n = 5; 13 vs. 80%; OR, 0.036; 95% CI, 0.002–0.741). Seven of eight patients with IT survived until discharge, with 29% showing a favorable functional outcome on day 90. Conclusions: Secondary deterioration is associated with poor outcome in patients with LVO and minor deficits, which in turn was associated with occlusion site. Future randomized controlled trials should assess whether selected patients, depending on occlusion site and associated characteristics, may benefit from MT.
Predictive Value of Multiparametric MRI for Response to Single-Cycle Induction Chemo-Immunotherapy in Locally Advanced Head and Neck Squamous Cell Carcinoma

Objectives To assess the predictive value of multiparametric MRI for treatment response evaluation of induction chemo-immunotherapy in locally advanced head and neck squamous cell carcinoma. Methods Twenty-two patients with locally advanced, histologically confirmed head and neck squamous cell carcinoma who were enrolled in the prospective multicenter phase II CheckRad-CD8 trial were included in the current analysis. In this unplanned secondary single-center analysis, all patients who received contrast-enhanced MRI at baseline and in week 4 after single-cycle induction therapy with cisplatin/docetaxel combined with the immune checkpoint inhibitors tremelimumab and durvalumab were included. In week 4, endoscopy with representative re-biopsy was performed to assess tumor response. All lesions were segmented in the baseline and restaging multiparametric MRI, including the primary tumor and lymph node metastases. The volume of interest of the respective lesions was volumetrically measured, and time-resolved mean intensities of the golden-angle radial sparse parallel-volume-interpolated gradient-echo perfusion (GRASP-VIBE) sequence were extracted. Additional quantitative parameters including the T1 ratio, short-TI inversion recovery ratio, apparent diffusion coefficient, and dynamic contrast-enhanced (DCE) values were measured. A model based on parallel random forests incorporating the MRI parameters from the baseline MRI was used to predict tumor response to therapy. Receiver operating characteristic (ROC) curves were used to evaluate the prognostic performance. Results Fifteen patients (68.2%) showed pathologic complete response in the re-biopsy, while seven patients had a residual tumor (31.8%). In all patients, the MRI-based primary tumor volume was significantly lower after treatment. The baseline DCE parameters of time to peak and wash-out were significantly different between the pathologic complete response group and the residual tumor group (p < 0.05). The developed model, based on parallel random forests and DCE parameters, was able to predict therapy response with a sensitivity of 78.7% (95% CI 71.24–84.93) and a specificity of 78.6% (95% CI 67.13–87.48). The model had an area under the ROC curve of 0.866 (95% CI 0.819–0.914). Conclusions DCE parameters indicated treatment response at follow-up, and a random forest machine learning algorithm based on DCE parameters was able to predict treatment response to induction chemo-immunotherapy.