bluuebunny/crossref_metadata_2025 huggingface dataset:
Do monocular myopia children need to wear glasses? Effects of monocular myopia on visual function and binocular balance
Authors: Xiang Aiqun , Du Kaixuan , Fu Qiuman , Zhang Yanni , Zhao Liting , Yan Li , Wen Dan
Published: March 2023

Objective

This study aims to compare the binocular visual functions and balance among monocular myopic adolescents and adults and binocular low myopic adolescents and explore whether monocular myopia requires glasses.

Methods

A total of 106 patients participated in this study. All patients were divided into three groups: the monocular myopia children group (Group 1 = 41 patients), the monocular myopia adult group (Group 2 = 26 patients) and the binocular low myopia children group (Group 3 = 39 patients). The refractive parameters, accommodation, stereopsis, and binocular balance were compared.

Results

The binocular refractive difference in Group 1, Group 2, and Group 3 was −1.37 ± 0.93, −1.94 ± 0.91, and −0.32 ± 0.27 D, respectively. Moreover, uncorrected visual acuity (UCVA), spherical equivalent (SE) and monocular accommodative amplitude (AA) between myopic and emmetropic eyes in Group 1 and Group 2 were significantly different (all P < 0.05). There was a significant difference in the accommodative facility (AF) between myopic and emmetropic eyes in Group 2 (t = 2.131, P = 0.043). Furthermore, significant differences were found in monocular AA (t = 6.879, P < 0.001), binocular AA (t = 5.043, P < 0.001) and binocular AF (t = −3.074, P = 0.003) between Group 1 and Group 2. The normal ratio of stereopsis according to the random dots test in Group 1 was higher than in Group 2 (χ2 = 14.596, P < 0.001). The normal ratio of dynamic stereopsis in Group 1 was lower than in Group 3 (χ2 = 13.281, P < 0.001). The normal signal-to-noise ratio of the binocular balance point in Group 1 was lower than Group 3 (χ2 = 4.755, P = 0.029).

Conclusion

First, monocular myopia could lead to accommodative dysfunction and unbalanced input of binocular visual signals, resulting in myopia progression. Second, monocular myopia may also be accompanied by stereopsis dysfunction, and long-term uncorrected monocular myopia may worsen stereopsis acuity in adulthood. In addition, patients with monocular myopia could exhibit stereopsis dysfunction at an early stage. Therefore, children with monocular myopia must wear glasses to restore binocular balance and visual functions, thereby delaying myopia progression.
Reactive oxygen species-responsive HET0016 prodrug-loaded liposomes attenuate neuroinflammation and improve neurological deficit in a rat model of juvenile traumatic brain injury
Authors: Qin Jun , Chen Xiaoli , Wang Rui , Tian Zedan , Li Yang , Shu Shiyu
Published: March 2023

The arachidonic acid pathway metabolite 20-hydroxyeicosatetraenoic acid (20-HETE) contributes to ischemia/reperfusion brain injury. Inhibition of 20-HETE formation can protect the developing brain from global ischemia. In previous studies, we have found that treatment with the 20-HETE synthesis inhibitor N-hydroxy-N-4-butyl-2-methylphenylformamidine (HET0016) can protect the immature brain from traumatic brain injury (TBI), but its hydrophobic nature limits its full potential. We designed a reactive oxygen species-responsive HET0016 prodrug, which consists of a thioketal link between HET0016 and stearyl alcohol (HET-TK-SA), and used the nanoprodrug strategy to successfully synthesize liposomes HET0016 prodrug liposomes (HPLs) to facilitate the application of HET0016 in protection from TBI. HPLs demonstrated spherical shape, size of about 127.8 nm, a zeta potential of −28.8 mv, a narrow particle size distribution and good stability. Male rats at postnatal day 16–17 underwent controlled cortical impact (CCI) followed by intravenous injection with vehicle or HET0016 (1 mg/kg, 2 h post-injury, once/day for 3 days). The results of the in vivo demonstrated that HPLs has good biosafety and can pass through the blood-brain barrier. Not only that compared with HET0016, HPLs better-inhibited inflammation and improved neuronal degeneration, which further led to lesion volume reduction, upgraded behavioral task performance, and ameliorated the degree of TBI impairment. Our results demonstrated HPLs could be a new strategy for juvenile TBI therapy.
Probiotic supplement as a promising strategy in early tau pathology prevention: Focusing on GSK-3β?
Authors: Flynn Cassandra M. , Yuan Qi
Published: March 2023

Neurofibrillary tangles (NFT) is one of the hallmarks of Alzheimer’s disease (AD). Recent research suggests that pretangle tau, the soluble precursor of NFT, is an initiator for AD pathogenesis, thus targeting pretangle tau pathology may be a promising early intervention focus. The bidirectional communications between the gut and the brain play a crucial role in health. The compromised gut-brain axis is involved in various neurodegenerative diseases including AD. However, most research on the relationship between gut microbiome and AD have focused on amyloid-β. In this mini review, we propose to target preclinical pretangle tau stages with gut microbiota interventions such as probiotic supplementation. We discuss the importance of targeting pretangle tau that starts decades before the onset of clinical symptoms, and potential intervention focusing on probiotic regulation of tau hyperphosphorylation. A particular focus is on GSK-3β, a protein kinase that is at the interface between tau phosphorylation, AD and diabetes mellitus.
Identification of an immune subtype-related prognostic signature of clear cell renal cell carcinoma based on single-cell sequencing analysis
Authors: Fan Zongyao , Xu Hewei , Ge Qingyu , Li Weilong , Zhang Junjie , Pu Yannan , Chen Zhengsen , Zhang Sicong , Xue Jun , Shen Baixin , Ding Liucheng , Wei Zhongqing
Published: March 2023

Background

There is growing evidence that immune cells are strongly associated with the prognosis and treatment of clear cell renal cell carcinoma (ccRCC). Our aim is to construct an immune subtype-related model to predict the prognosis of ccRCC patients and to provide guidance for finding appropriate treatment strategies.

Methods

Based on single-cell analysis of the GSE152938 dataset from the GEO database, we defined the immune subtype-related genes in ccRCC. Immediately afterwards, we used Cox regression and Lasso regression to build a prognostic model based on TCGA database. Then, we carried out a series of evaluation analyses around the model. Finally, we proved the role of VMP1 in ccRCC by cellular assays.

Result

Initially, based on TCGA ccRCC patient data and GEO ccRCC single-cell data, we successfully constructed a prognostic model consisting of five genes. Survival analysis showed that the higher the risk score, the worse the prognosis. We also found that the model had high predictive accuracy for patient prognosis through ROC analysis. In addition, we found that patients in the high-risk group had stronger immune cell infiltration and higher levels of immune checkpoint gene expression. Finally, cellular experiments demonstrated that when the VMP1 gene was knocked down, 786-O cells showed reduced proliferation, migration, and invasion ability and increased levels of apoptosis.

Conclusion

Our study can provide a reference for the diagnosis and treatment of patients with ccRCC.
Case report: Epithelioid inflammatory myofibroblastic sarcoma treated with an ALK TKI ensartinib
Authors: Li Mengmeng , Xing Ruyue , Huang Jiuyan , Shi Chao , Wei Chunhua , Wang Huijuan
Published: March 2023

Epithelioid inflammatory myofibroblastic sarcoma (EIMS) is an aggressive variant of inflammatory myofibroblastic tumor (IMT) and has a poor prognosis. EIMS is characterized by epithelioid morphology, neutrophilic infiltrate and specific fusion partners of anaplastic lymphoma kinase (ALK). Despite no standard therapy for EIMS, ALK tyrosine kinase inhibitors (TKIs) are recommended for these tumors. The present case describes an abdominal mass that presented in a 31-year-old male. The patient suffered from recurrence and multiple metastases 2 months after surgery. Ensartinib was administered and RANBP2-ALK fusion was detected. A partial response has been observed for 4 months and there has been no recurrence. This study provided a successful case with sustained response of targeted therapy.
Identification and diagnosis of mammographic malignant architectural distortion using a deep learning based mask regional convolutional neural network
Authors: Liu Yuanyuan , Tong Yunfei , Wan Yun , Xia Ziqiang , Yao Guoyan , Shang Xiaojing , Huang Yan , Chen Lijun , Chen Daniel Q. , Liu Bo
Published: March 2023

Background

Architectural distortion (AD) is a common imaging manifestation of breast cancer, but is also seen in benign lesions. This study aimed to construct deep learning models using mask regional convolutional neural network (Mask-RCNN) for AD identification in full-field digital mammography (FFDM) and evaluate the performance of models for malignant AD diagnosis.

Methods

This retrospective diagnostic study was conducted at the Second Affiliated Hospital of Guangzhou University of Chinese Medicine between January 2011 and December 2020. Patients with AD in the breast in FFDM were included. Machine learning models for AD identification were developed using the Mask RCNN method. Receiver operating characteristics (ROC) curves, their areas under the curve (AUCs), and recall/sensitivity were used to evaluate the models. Models with the highest AUCs were selected for malignant AD diagnosis.

Results

A total of 349 AD patients (190 with malignant AD) were enrolled. EfficientNetV2, EfficientNetV1, ResNext, and ResNet were developed for AD identification, with AUCs of 0.89, 0.87, 0.81 and 0.79. The AUC of EfficientNetV2 was significantly higher than EfficientNetV1 (0.89 vs. 0.78, P=0.001) for malignant AD diagnosis, and the recall/sensitivity of the EfficientNetV2 model was 0.93.

Conclusion

The Mask-RCNN-based EfficientNetV2 model has a good diagnostic value for malignant AD.
Correlation between the timing of diagnostic ureteroscopy for upper tract urothelial cancer and intravesical recurrence after radical nephroureterectomy
Authors: Luo Zhenkai , Jiao Binbin , Su Caixia , Zhao Hang , Yan Yangxuanyu , Pan Yijin , Ren Jian , Zhang Guan , Ding Zhenshan
Published: March 2023

Objective

We aimed to evaluate the effect of the timing of diagnostic ureteroscopy (URS) on intravesical recurrence (IVR) following radical nephroureterectomy (RNU).

Patients and methods

The clinical data of 220 patients with upper tract urothelial carcinoma (UTUC) treated with RNU at our center from June 2010 to December 2020 were retrospectively analyzed. According to the timing of the URS, all patients were divided into three groups: the no URS group, the 1-session group (diagnostic URS immediately followed by RNU), and the 2-session group (RNU after diagnostic URS). Additionally, we analyzed IVR-free survival (IVRFS) using the Kaplan-Meier and Cox proportional regression methods.

Results

The median follow-up period of these 220 patents was 41 (range: 2-143) months. Among them, 58 patients developed IVR following RNU. Kaplan-Meier curve displayed a significantly higher IVR rate in both treatment groups than in the no-URS group (p=0.025). In the subgroup of patients with renal pelvis cancer, the incidence of IVR was significantly higher in both treatment groups than in the group without URS (p=0.006). In univariate Cox proportional regression analysis, the two treatment groups were risk factors for IVR compared to the no-URS group [p=0.027, hazard ratio (HR): 1.93, 95% confidence interval (CI): 1.08-3.46]. The two-stage group (p=0.032, HR: 1.98, 95% CI: 1.08-3.65), positive urine pathology (p<0.001, HR: 8.12, 95% CI: 3.63-18.15), adjuvant chemotherapy (p<0.001, HR: 0.20, 95% CI: 0.10-0.38), and positive margin (p<0.0001, HR: 7.50, 95% CI: 2.44-23.08) were all identified as independent predictors in the multivariate.

Conclusion

This study revealed that delayed RNU following diagnostic URS may increase the risk of postoperative IVR in patients with UTUC, preoperatively positive uropathology, and positive surgical margin were risk factors for IVR after RNU, while early postoperative chemotherapy may effectively prevent IVR. Delay of RUN after URS could increase the risk of IVR.
An analysis of the distribution and spectrum of alpha thalassemia mutations in Rasht City, North of Iran
Authors: Asghari Ahmadabad Mona , Pourreza Noushin , Ramezanpour Setareh , Baghersalimi Adel , Enshaei Mersedeh , Askari Marjan , Alizadeh Amirhossein , Izadi Elahe , Darbandi Bahram
Published: March 2023

Background

Alpha thalassemia is one of the most common hereditary hemoglobin disorders worldwide, particularly in the Middle East, including Iran. Therefore, determining the spectrum and distribution of alpha thalassemia mutation is a fundamental component of preventive approaches and management strategies.

Methods

The present study reviews the genetic testing and blood laboratory results of 455 candidates eligible for marriage who were suspected of being thalassemia carriers and on whom genetic testing was performed from 21 March 2013 to 31 December 2020 in Rasht City.

Results

A total of 114 (25.05%) alpha thalassemia cases were identified. Fifteen different alpha mutations were found. The most common mutation among the study population was −α3.7 deletion in 55 patients (48.24%), followed by Hb Constant Spring (C.S) in 21 patients (18.42%) and poly A2 in 16 (14.03%). Also, most of the patients were silent carriers. The deletion type of mutation was much more common than non-deletion mutations.

Conclusion

Our study reveals genetic heterogeneity and alpha thalassemia diversity among the Rasht City population. We expect that these findings will help guide premarital screening and genetic counseling, prenatal diagnosis of thalassemia, preventive strategy development, as well as a compilation of the alpha thalassemia catalog in Guilan province.
Pyelo-ureteral junction obstruction in poorly functioning kidneys: Does conservative management play a role in pediatric patients?
Authors: Zarfati Angelo , Mele Ermelinda , Villani Maria Felicia , Capozza Nicola , Castagnetti Marco
Published: March 2023

Background

Management of Pyelo-ureteral Junction Obstruction (PUJO) in poorly functioning kidneys in pediatric patients is still controversial, particularly regarding the role of conservative treatment.

Aim

To evaluate and present the outcomes of internal diversion and follow-up results of a small series of pediatric patients with UPJO in poorly functioning kidneys.

Study design

Retrospective review of 17 consecutive patients with unilateral PUJO in kidneys with Differential Renal Function (DRF) <20% undergoing temporary internal urinary diversion between 2009 and 2021 at a single tertiary center. DRF was reassessed after 1–3 months of diversion and subsequent management was conservative or surgical (pyeloplasty or nephrectomy) based on surgeon’s and family’s preferences without randomization.

Results

After a trial of internal urinary diversion, 4/17 patients (23%) showed a DRF increase ≥5% (9%–12%), up to a maximum DRF of 28%, 3 underwent pyeloplasty, while 1 was managed conservatively. The remaining 13 patients showed no differential renal function improvement after diversion, and 7 were managed expectantly while 6 surgically (4 pyeloplasty, 2 nephrectomy). Overall, nine patients (53%) were managed surgically and 8 (47%) expectantly After a median (range) follow-up of 3.1 (0.3–7.9) years, no significant difference was observed between groups regarding symptoms (p = 0.205), need for further surgery (p = 1.000), and renal function (p = 1.000).

Discussion

Although fraught with the limitation of a small sample size, this is the first study reporting on the conservative management of this controversial group of patients.

Conclusion

In present pediatric series of pyelo-ureteral Junction obstruction in poorly functioning kidneys with differential renal function <20%, function recovery after a trial of internal urinary diversion was quite exceptional, and no difference was observed in outcome between patients managed surgically and conservatively after stent removal.
Tailored treatments in inborn errors of immunity associated with atopy (IEIs-A) with skin involvement
Authors: Giancotta Carmela , Colantoni Nicole , Pacillo Lucia , Santilli Veronica , Amodio Donato , Manno Emma Concetta , Cotugno Nicola , Rotulo Gioacchino Andrea , Rivalta Beatrice , Finocchi Andrea , Cancrini Caterina , Diociaiuti Andrea , El Hachem May , Zangari Paola
Published: March 2023

Inborn errors of immunity associated with atopy (IEIs-A) are a group of inherited monogenic disorders that occur with immune dysregulation and frequent skin involvement. Several pathways are involved in the pathogenesis of these conditions, including immune system defects, alterations of skin barrier and metabolism perturbations. Current technological improvements and the higher accessibility to genetic testing, recently allowed the identification of novel molecular pathways involved in IEIs-A, also informing on potential tailored therapeutic strategies. Compared to other systemic therapy for skin diseases, biologics have the less toxic and the best tolerated profile in the setting of immune dysregulation. Here, we review IEIs-A with skin involvement focusing on the tailored therapeutic approach according to their pathogenetic mechanism.
Therapeutic potential of TRPM8 channels in cancer treatment
Authors: Ochoa Sara V. , Casas Zulma , Albarracín Sonia L. , Sutachan Jhon Jairo , Torres Yolima P.
Published: March 2023

Cancer is a multifactorial process associated with changes in signaling pathways leading to cell cycle variations and gene expression. The transient receptor potential melastatin 8 (TRPM8) channel is a non-selective cation channel expressed in neuronal and non-neuronal tissues, where it is involved in several processes, including thermosensation, differentiation, and migration. Cancer is a multifactorial process associated with changes in signaling pathways leading to variations in cell cycle and gene expression. Interestingly, it has been shown that TRPM8 channels also participate in physiological processes related to cancer, such as proliferation, survival, and invasion. For instance, TRPM8 channels have an important role in the diagnosis, prognosis, and treatment of prostate cancer. In addition, it has been reported that TRPM8 channels are involved in the progress of pancreatic, breast, bladder, colon, gastric, and skin cancers, glioblastoma, and neuroblastoma. In this review, we summarize the current knowledge on the role of TRPM8 channels in cancer progression. We also discuss the therapeutic potential of TRPM8 in carcinogenesis, which has been proposed as a molecular target for cancer therapy.
Effect of mTOR inhibitors on sodium taurocholate cotransporting polypeptide (NTCP) function in vitro
Authors: Saran Chitra , Ho Henry , Honkakoski Paavo , Brouwer Kim L. R.
Published: March 2023

The sodium taurocholate cotransporting polypeptide (NTCP; gene name SLC10A1) is the primary hepatic basolateral uptake transporter for conjugated bile acids and the entry receptor for the hepatitis B and D virus (HBV/HDV). Regulation of human NTCP remains a knowledge gap due to significant species differences in substrate and inhibitor selectivity and plasma membrane expression. In the present study, various kinase inhibitors were screened for inhibition of NTCP function and taurocholate (TCA) uptake using NTCP-transfected HuH-7 cells. This study identified everolimus, an mTOR inhibitor and macrocyclic immunosuppressive drug, as an NTCP inhibitor with modest potency (IC50 = 6.7–8.0 µM). Further investigation in differentiated HuH-7 cells expressing NTCP and NTCP-overexpressing Flp-In T-REx 293 cells revealed that the mechanism of action of everolimus on NTCP is direct inhibition and mTOR-independent. Structural analogs of everolimus inhibited NTCP-mediated TCA uptake, however, functional analogs did not affect NTCP-mediated TCA transport, providing further evidence for direct inhibition. This work contributes to the growing body of literature suggesting that NTCP-mediated bile acid uptake may be inhibited by macrocyclic peptides, which may be further exploited to develop novel medications against HBV/HDV.
Nirmatrelvir/ritonavir for patients with SARS-CoV-2 infection and impaired kidney function during the Omicron surge
Authors: Yan Jiayi , Cai Hong , Wang Jieying , Zhu Mingli , Li Ping , Li Peiying , Wu Bin , Che Xiajing , Gu Leyi , Mou Shan
Published: March 2023

Background: Nirmatrelvir/ritonavir has demonstrated effectiveness in high-risk patients with coronavirus disease 2019 (COVID-19). However, investigations on the efficacy and safety of nirmatrelvir/ritonavir in patients with kidney dysfunction are limited.

Methods: Data were collected from the patients admitted to a COVID-19 referral center in Shanghai, China. Patients were at least 18 years of age and had a baseline estimated glomerular filtration rate (eGFR) of <60 ml/min/1·73 m2. The primary endpoint was a composite of all-cause mortality, intensive care unit admission, or cardiovascular events. The secondary endpoint was viral shedding.

Results: Among the 195 participants, 73 received nirmatrelvir/ritonavir. A lower risk of the primary endpoint was observed in nirmatrelvir/ritonavir recipients compared with non-recipients [adjusted HR 0.56 (95% CI: 0.32–0.96); p = 0.035]. Nirmatrelvir/ritonavir recipients experienced a shorter duration of viral shedding [adjusted HR 3·70 (95%CI: 2.60–5.28); p < 0.001) and faster viral load clearance versus non-recipients. Among the nirmatrelvir/ritonavir users, earlier initiation of nirmatrelvir/ritonavir within 5 days since COVID-19 diagnosis was related with shorter viral shedding time (adjusted HR 7.84 [95% CI: 3.28–18.76]; p < 0.001) compared to late initiation. No patients reported serious adverse events during treatment.

Conclusion: Our findings support the early initiation of nirmatrelvir/ritonavir for high-risk patients with impaired kidney function. This could improve patient outcomes and shorten the viral shedding period.
Comparison of cardiac image-derived input functions for quantitative whole body [18F]FDG imaging with arterial blood sampling
Authors: Reed Murray Bruce , Godbersen Godber Mathis , Vraka Chrysoula , Rausch Ivo , Ponce de León Magdalena , Popper Valentin , Geist Barbara , Nics Lukas , Komorowski Arkadiusz , Karanikas Georgios , Beyer Thomas , Traub-Weidinger Tatjana , Hahn Andreas , Langsteger Werner , Hacker Marcus , Lanzenberger Rupert
Published: March 2023

Introduction: Dynamic positron emission tomography (PET) and the application of kinetic models can provide important quantitative information based on its temporal information. This however requires arterial blood sampling, which can be challenging to acquire. Nowadays, state-of-the-art PET/CT systems offer fully automated, whole-body (WB) kinetic modelling protocols using image-derived input functions (IDIF) to replace arterial blood sampling. Here, we compared the validity of an automatic WB kinetic model protocol to the reference standard arterial input function (AIF) for both clinical and research settings.

Methods: Sixteen healthy participants underwent dynamic WB [18F]FDG scans using a continuous bed motion PET/CT system with simultaneous arterial blood sampling. Multiple processing pipelines that included automatic and manually generated IDIFs derived from the aorta and left ventricle, with and without motion correction were compared to the AIF. Subsequently generated quantitative images of glucose metabolism were compared to evaluate performance of the different input functions.

Results: We observed moderate to high correlations between IDIFs and the AIF regarding area under the curve (r = 0.49–0.89) as well as for the cerebral metabolic rate of glucose (CMRGlu) (r = 0.68–0.95). Manual placing of IDIFs and motion correction further improved their similarity to the AIF.

Discussion: In general, the automatic vendor protocol is a feasible approach for the quantification of CMRGlu for both, clinical and research settings where expertise or time is not available. However, we advise on a rigorous inspection of the placement of the volume of interest, the resulting IDIF, and the quantitative values to ensure valid interpretations. In protocols requiring longer scan times or where cohorts are prone to involuntary movement, manual IDIF definition with additional motion correction is recommended, as this has greater accuracy and reliability.
Concurrent validity of machine learning-classified functional upper extremity use from accelerometry in chronic stroke
Authors: Geed Shashwati , Grainger Megan L. , Mitchell Abigail , Anderson Cassidy C. , Schmaulfuss Henrike L. , Culp Seraphina A. , McCormick Eilis R. , McGarry Maureen R. , Delgado Mystee N. , Noccioli Allysa D. , Shelepov Julia , Dromerick Alexander W. , Lum Peter S.
Published: March 2023

Objective:This study aims to investigate the validity of machine learning-derived amount of real-world functional upper extremity (UE) use in individuals with stroke. We hypothesized that machine learning classification of wrist-worn accelerometry will be as accurate as frame-by-frame video labeling (ground truth). A second objective was to validate the machine learning classification against measures of impairment, function, dexterity, and self-reported UE use.

Design:Cross-sectional and convenience sampling.

Setting:Outpatient rehabilitation.

Participants:Individuals (>18 years) with neuroimaging-confirmed ischemic or hemorrhagic stroke >6-months prior (n= 31) with persistent impairment of the hemiparetic arm and upper extremity Fugl-Meyer (UEFM) score = 12–57.

Methods:Participants wore an accelerometer on each arm and were video recorded while completing an “activity script” comprising activities and instrumental activities of daily living in a simulated apartment in outpatient rehabilitation. The video was annotated to determine the ground-truth amount of functional UE use.

Main outcome measures:The amount of real-world UE use was estimated using a random forest classifier trained on the accelerometry data. UE motor function was measured with the Action Research Arm Test (ARAT), UEFM, and nine-hole peg test (9HPT). The amount of real-world UE use was measured using the Motor Activity Log (MAL).

Results:The machine learning estimated use ratio was significantly correlated with the use ratio derived from video annotation, ARAT, UEFM, 9HPT, and to a lesser extent, MAL. Bland–Altman plots showed excellent agreement between use ratios calculated from video-annotated and machine-learning classification. Factor analysis showed that machine learning use ratios capture the same construct as ARAT, UEFM, 9HPT, and MAL and explain 83% of the variance in UE motor performance.

Conclusion:Our machine learning approach provides a valid measure of functional UE use. The accuracy, validity, and small footprint of this machine learning approach makes it feasible for measurement of UE recovery in stroke rehabilitation trials.
Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod
Authors: Eide Marta , Goksøyr Anders , Yadetie Fekadu , Gilabert Alejandra , Bartosova Zdenka , Frøysa Håvard G. , Fallahi Shirin , Zhang Xiaokang , Blaser Nello , Jonassen Inge , Bruheim Per , Alendal Guttorm , Brun Morten , Porte Cinta , Karlsen Odd André
Published: March 2023

Lipid metabolism is essential in maintaining energy homeostasis in multicellular organisms. In vertebrates, the peroxisome proliferator-activated receptors (PPARs, NR1C) regulate the expression of many genes involved in these processes. Atlantic cod (Gadus morhua) is an important fish species in the North Atlantic ecosystem and in human nutrition, with a highly fatty liver. Here we study the involvement of Atlantic cod Ppar a and b subtypes in systemic regulation of lipid metabolism using two model agonists after in vivo exposure. WY-14,643, a specific PPARA ligand in mammals, activated cod Ppara1 and Ppara2 in vitro. In vivo, WY-14,643 caused a shift in lipid transport both at transcriptional and translational level in cod. However, WY-14,643 induced fewer genes in the fatty acid beta-oxidation pathway compared to that observed in rodents. Although GW501516 serves as a specific PPARB/D ligand in mammals, this compound activated cod Ppara1 and Ppara2 as well as Pparb in vitro. In vivo, it further induced transcription of Ppar target genes and caused changes in lipid composition of liver and plasma. The integrative approach provide a foundation for understanding how Ppars are engaged in regulating lipid metabolism in Atlantic cod physiology. We have shown that WY-14,643 and GW501516 activate Atlantic cod Ppara and Pparb, affect genes in lipid metabolism pathways, and induce changes in the lipid composition in plasma and liver microsomal membranes. Particularly, the combined transcriptomic, proteomics and lipidomics analyses revealed that effects of WY-14,643 on lipid metabolism are similar to what is known in mammalian studies, suggesting conservation of Ppara functions in mediating lipid metabolic processes in fish. The alterations in the lipid profiles observed after Ppar agonist exposure suggest that other chemicals with similar Ppar receptor affinities may cause disturbances in the lipid regulation of fish. Model organism: Atlantic cod (Gadus morhua). LSID: urn:lsid:zoobank.org:act:389BE401-2718-4CF2-BBAE-2E13A97A5E7B. COL Identifier: 6K72F.
Variable organization of symbiont-containing tissue across planthoppers hosting different heritable endosymbionts
Authors: Michalik Anna , Franco Diego Castillo , Deng Junchen , Szklarzewicz Teresa , Stroiński Adam , Kobiałka Michał , Łukasik Piotr
Published: March 2023

Sap-feeding hemipteran insects live in associations with diverse heritable symbiotic microorganisms (bacteria and fungi) that provide essential nutrients deficient in their hosts’ diets. These symbionts typically reside in highly specialized organs called bacteriomes (with bacterial symbionts) or mycetomes (with fungal symbionts). The organization of these organs varies between insect clades that are ancestrally associated with different microbes. As these symbioses evolve and additional microorganisms complement or replace the ancient associates, the organization of the symbiont-containing tissue becomes even more variable. Planthoppers (Hemiptera: Fulgoromorpha) are ancestrally associated with bacterial symbionts Sulcia and Vidania, but in many of the planthopper lineages, these symbionts are now accompanied or have been replaced by other heritable bacteria (e.g., Sodalis, Arsenophonus, Purcelliella) or fungi. We know the identity of many of these microbes, but the symbiont distribution within the host tissues and the bacteriome organization have not been systematically studied using modern microscopy techniques. Here, we combine light, fluorescence, and transmission electron microscopy with phylogenomic data to compare symbiont tissue distributions and the bacteriome organization across planthoppers representing 15 families. We identify and describe seven primary types of symbiont localization and seven types of the organization of the bacteriome. We show that Sulcia and Vidania, when present, usually occupy distinct bacteriomes distributed within the body cavity. The more recently acquired gammaproteobacterial and fungal symbionts generally occupy separate groups of cells organized into distinct bacteriomes or mycetomes, distinct from those with Sulcia and Vidania. They can also be localized in the cytoplasm of fat body cells. Alphaproteobacterial symbionts colonize a wider range of host body habitats: Asaia-like symbionts often colonize the host gut lumen, whereas Wolbachia and Rickettsia are usually scattered across insect tissues and cell types, including cells containing other symbionts, bacteriome sheath, fat body cells, gut epithelium, as well as hemolymph. However, there are exceptions, including Gammaproteobacteria that share bacteriome with Vidania, or Alphaproteobacteria that colonize Sulcia cells. We discuss how planthopper symbiont localization correlates with their acquisition and replacement patterns and the symbionts’ likely functions. We also discuss the evolutionary consequences, constraints, and significance of these findings.
Beyond cannabinoids: Application of NMR-based metabolomics for the assessment of Cannabis sativa L. crop health
Authors: Fernández Santiago , Castro Rossina , López-Radcenco Andrés , Rodriguez Paula , Carrera Inés , García-Carnelli Carlos , Moyna Guillermo
Published: March 2023

While Cannabis sativa L. varieties have been traditionally characterized by their major cannabinoid profile, it is now well established that other plant metabolites can also have physiological effects, including minor cannabinoids, terpenes, and flavonoids. Given the multiple applications of cannabis in the medical field, it is therefore critical to characterize it according to its chemical composition (i.e., its metabolome) and not only its botanical traits. With this in mind, the cannabinoid and metabolomic profiles from inflorescences of two C. sativa varieties with either high Δ9-tetrahydrocannabinolic acid (THCA) or high cannabidiolic acid (CBDA) contents harvested at different times were studied. According to results from HPLC and NMR-based untargeted metabolomic analyses of organic and aqueous plant material extracts, we show that in addition to expected variations according to cannabinoid profiles, it is possible to distinguish between harvests of the same variety. In particular, it was possible to correlate variations in the metabolome with presence of powdery mildew, leading to the identification of molecular markers associated with this fungal infection in C. sativa.
Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana (Musa acuminata L. AAA group, cv. Cavendish)
Authors: Wang Zhuo , Yao Xiao-ming , Jia Cai-hong , Xu Bi-yu , Wang Jing-yi , Liu Ju-hua , Jin Zhi-qiang
Published: March 2023

Background

Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses.

Results

In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in Musa acuminata genome and found the number of MaCOMT gene family was the largest, while MaC3Hs had only two members. MaPALs retained the original members, and the number of Ma4CLs in lignin biosynthesis was significantly less than that of flavonoids. Segmental duplication existed in most gene families, except for MaC3Hs, and tandem duplication was the main way to expand the number of MaCOMTs. Moreover, the expression profiles of lignin biosynthesis genes during fruit development, postharvest ripening stages and under various abiotic and biological stresses were investigated using available RNA-sequencing data to obtain fruit ripening and stress response candidate genes. Finally, a co-expression network of lignin biosynthesis genes was constructed by weighted gene co-expression network analysis to elucidate the lignin biosynthesis genes that might participate in lignin biosynthesis in banana during development and in response to stresses.

Conclusion

This study systematically identified the lignin biosynthesis genes in the Musa acuminata genome, providing important candidate genes for further functional analysis. The identification of the major genes involved in lignin biosynthesis in banana provides the basis for the development of strategies to improve new banana varieties tolerant to biological and abiotic stresses with high yield and high quality.
ZmHOX32 is related to photosynthesis and likely functions in plant architecture of maize
Authors: Miao Xinxin , Zhu Wanchao , Jin Qixiao , Song Zemeng , Li Lin
Published: March 2023

HOX32, a member of the HD-ZIP III family, functions in the leaf morphogenesis and plant photosynthesis. However, the regulatory mechanism of HOX32 in maize has not been studied and the regulatory relationship in photosynthesis is unclear. We conducted a comprehensive study, including phylogenetic analysis, expression profiling at both transcriptome and translatome levels, subcellular localization, tsCUT&Tag, co-expression analysis, and association analysis with agronomic traits on HOX32 for the dissection of the functional roles of HOX32. ZmHOX32 shows conservation in plants. As expected, maize HOX32 protein is specifically expressed in the nucleus. ZmHOX32 showed constitutively expression at both transcriptome and translatome levels. We uncovered the downstream target genes of ZmHOX32 by tsCUT&Tag and constructed a cascaded regulatory network combining the co-expression networks. Both direct and indirect targets of ZmHOX32 showed significant gene ontology enrichment in terms of photosynthesis in maize. The association study suggested that ZmHOX32 plays an important role in regulation of plant architecture. Our results illustrate a complex regulatory network of HOX32 involving in photosynthesis and plant architecture, which deepens our understanding of the phenotypic variation in plants.
Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects with large datasets in white spruce
Authors: Nadeau Simon , Beaulieu Jean , Gezan Salvador A. , Perron Martin , Bousquet Jean , Lenz Patrick R. N.
Published: March 2023

Introduction

Genomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains.

Methods

Using two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models.

Results

While wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely.

Discussion

This study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material.
Evolution of seed characters and of dispersal modes in Aizoaceae
Authors: Sukhorukov Alexander P. , Nilova Maya V. , Kushunina Maria , Mazei Yuri , Klak Cornelia
Published: March 2023

The family Aizoaceae includes ~1880 species and is one of the more diverse groups within Caryophyllales, particularly in arid areas in the western part of southern Africa. Most species are dwarf succulent-leaf shrubs. In response to the harsh climatic conditions prevalent where they occur, many representatives have evolved special reproductive adaptations. These include hygrochastic capsules (mostly found in Mesembryanthemoideae and Ruschioideae), burr-like indehiscent and one-seeded, winged diaspores, and fast germination of seeds after rain. We focused on anatomical features, evolutionary trends, and the ecological significance of various morpho-anatomical structures found in the seeds. The seeds of 132 species from 61 genera were studied, and 18 diagnostic characters were discovered. All studied characters were compared with those of other families from core Caryophyllales. The seed notch and embryo shape were added to the list of characteristics distinguishing major clades within the family. In addition, the presence of longitudinal ridges and a keel on the seed are additional characters of Aizooideae and combined Ruschioideae-Apatesieae, respectively. Puzzle-like borders of testa cells are a common trait in Ruschioideae and Mesembryanthemoideae. Most taxa in Aizoaceae have a thin seed coat, which is the ancestral state within the family. This may facilitate fast germination. We observed several shifts to a medium-thick or thick seed coat in members of Ruschioideae and Acrosanthoideae. These inhabit fire-prone environments (in vegetation types known asfynbosandrenosterveld), where the thickened seed coat may protect against damage by fire. Multi-seeded fruits are the ancestral state within Aizoaceae, with several shifts to one-(two-)seeded xerochastic fruits. The latter are dispersedviaautochory, zoochory, or anemochory. This trait has evolved mainly in less succulent subfamilies Acrosanthoideae, Aizooideae, and Sesuvioideae. In highly succulent subfamilies Ruschioideae and Mesembryanthemoideae, fruits are almost exclusively multi-seeded and hygrochastic with ombrohydrochoric dispersal. A reduction in the number of seeds within a dispersal unit is rare. Within Apatesieae and Ruschieae, there are also a few unusual genera whose fruits fall apart into one- to two-seeded mericarps (that are mainly dispersed by wind).
Boosting precision crop protection towards agriculture 5.0 via machine learning and emerging technologies: A contextual review
Authors: Mesías-Ruiz Gustavo A. , Pérez-Ortiz María , Dorado José , de Castro Ana I. , Peña José M.
Published: March 2023

Crop protection is a key activity for the sustainability and feasibility of agriculture in a current context of climate change, which is causing the destabilization of agricultural practices and an increase in the incidence of current or invasive pests, and a growing world population that requires guaranteeing the food supply chain and ensuring food security. In view of these events, this article provides a contextual review in six sections on the role of artificial intelligence (AI), machine learning (ML) and other emerging technologies to solve current and future challenges of crop protection. Over time, crop protection has progressed from a primitive agriculture 1.0 (Ag1.0) through various technological developments to reach a level of maturity closelyin line with Ag5.0 (section 1), which is characterized by successfully leveraging ML capacity and modern agricultural devices and machines that perceive, analyze and actuate following the main stages of precision crop protection (section 2). Section 3 presents a taxonomy of ML algorithms that support the development and implementation of precision crop protection, while section 4 analyses the scientific impact of ML on the basis of an extensive bibliometric study of >120 algorithms, outlining the most widely used ML and deep learning (DL) techniques currently applied in relevant case studies on the detection and control of crop diseases, weeds and plagues. Section 5 describes 39 emerging technologies in the fields of smart sensors and other advanced hardware devices, telecommunications, proximal and remote sensing, and AI-based robotics that will foreseeably lead the next generation of perception-based, decision-making and actuation systems for digitized, smart and real-time crop protection in a realistic Ag5.0. Finally, section 6 highlights the main conclusions and final remarks.
Integration of GWAS, linkage analysis and transcriptome analysis to reveal the genetic basis of flowering time-related traits in maize
Authors: Wu Xun , Liu Ying , Lu Xuefeng , Tu Liang , Gao Yuan , Wang Dong , Guo Shuang , Xiao Yifei , Xiao Pingfang , Guo Xiangyang , Wang Angui , Liu Pengfei , Zhu Yunfang , Chen Lin , Chen Zehui
Published: March 2023

Maize (Zea mays) inbred lines vary greatly in flowering time, but the genetic basis of this variation is unknown. In this study, three maize flowering-related traits (DTT, days to tasselling; DTP, days to pollen shed; DTS, days to silking) were evaluated with an association panel consisting of 226 maize inbred lines and an F2:3 population with 120 offspring from a cross between the T32 and Qi319 lines in different environments. A total of 82 significant single nucleotide polymorphisms (SNPs) and 117 candidate genes were identified by genome-wide association analysis. Twenty-one quantitative trait loci (QTLs) and 65 candidate genes were found for maize flowering time by linkage analysis with the constructed high-density genetic map. Transcriptome analysis was performed for Qi319, which is an early-maturing inbred line, and T32, which is a late-maturing inbred line, in two different environments. Compared with T32, Qi319 showed upregulation of 3815 genes and downregulation of 3906 genes. By integrating a genome-wide association study (GWAS), linkage analysis and transcriptome analysis, 25 important candidate genes for maize flowering time were identified. Together, our results provide an important resource and a foundation for an enhanced understanding of flowering time in maize.
Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae)
Authors: Zhou Lisi , Chen Tongyao , Qiu Xiandan , Liu Jinxin , Guo Shunxing
Published: March 2023

Introduction

Galeola lindleyana is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae.

Methods

In this study, the G. lindleyana plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes.

Results

The G. lindleyana plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and psaJ in photosystem I. The length of the G. lindleyana plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid’s plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two ndhB genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the Cyrtosia septentrionalis plastome which was found to be closest in length to the G. lindleyana plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the psbA, psbK, atpA and psaB retained in the G. lindleyana plastome were missing in the C. septentrionalis plastome, while, the matK, rps16, and atpF were incomplete in the C. septentrionalis plastome, yet still complete in that of the G. lindleyana. Lastly, compared with the G. lindleyana plastome, a 15 kb region located in the SSC area between ndhB-rrn16S was found to be inverted in the C. septentrionalis plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes.

Discussion

Thus, this study’s decoding of the mycoheterotrophic G. lindleyana plastome provides valuable resource data for future research and conservation of endangered orchids.