Prospects and challenges of cancer systems medicine: from genes to disease networks.

It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.

CRISPR-Cas9 technology: As an efficient genome modification tool in the cancer diagnosis and treatment.

Cancer is the second most common cause of death globally and is a major public health concern. Managing this disease is difficult due to its multiple stages and numerous genetic and epigenetic changes. Traditional cancer diagnosis and treatment methods have limitations, making it crucial to develop new modalities to combat the increasing burden of cancer. The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has transformed genetic engineering due to its simplicity, specificity, low cytotoxicity, and cost-effectiveness. It has been proposed as an effective technology to enhance cancer diagnosis and treatment strategies. This article presents the most recent discoveries regarding the structure, mechanism, and delivery methods of the highly powerful genome editing tool, CRISPR-Cas9. In terms of diagnosis, the article examines the role of CRISPR-Cas9 in detecting microRNAs and DNA methylation, and discusses two popular gene detection techniques that utilize the CRISPR-Cas system: DNA endonuclease-targeted CRISPR trans reporter and specific high sensitivity enzymatic reporter unlocking. Regarding treatment, the article explores several genes that have been identified and modified by CRISPR-Cas9 for effective tumorigenesis of common cancers such as breast, lung, and colorectal cancer. The present review also addresses the challenges and ethical issues associated with using CRISPR-Cas9 as a diagnostic and therapeutic tool. Despite some limitations, CRISPR-Cas9-based cancer diagnosis has the potential to become the next generation of cancer diagnostic tools, and the continuous progress of CRISPR-Cas9 can greatly aid in cancer treatment.

Lipid variability and risk of microvascular complications in patients with diabetes: a systematic review and meta-analysis.

BACKGROUND AND AIMS: The current systematic review aimed to elucidate the effects of lipid variability on microvascular complication risk in diabetic patients. The lipid components studied were as follows: High-density lipoprotein (HDL), High-density lipoprotein (LDL), Triglyceride (TG), Total Cholesterol (TC), and Remnant Cholesterol (RC). METHOD: We carried out a systematic search in multiple databases, including PubMed, Web of Science, and SCOPUS, up to October 2nd, 2023. After omitting the duplicates, we screened the title and abstract of the studies. Next, we retrieved and reviewed the full text of the remaining articles and included the ones that met our inclusion criteria in the study. RESULT: In this research, we examined seven studies, comprising six cohort studies and one cross-sectional study. This research was conducted in Hong Kong, China, Japan, Taiwan, Finland, and Italy. The publication years of these articles ranged from 2012 to 2022, and the duration of each study ranged from 5 to 14.3 years. The study group consisted of patients with type 2 diabetes aged between 45 and 84 years, with a diabetes history of 7 to 12 years. These studies have demonstrated that higher levels of LDL, HDL, and TG variability can have adverse effects on microvascular complications, especially nephropathy and neuropathic complications. TG and LDL variability were associated with the development of albuminuria and GFR decline. Additionally, reducing HDL levels showed a protective effect against microalbuminuria. However, other studies did not reveal an apparent relationship between lipid variations and microvascular complications, such as retinopathy. Current research lacks geographic and demographic diversity. Increased HDL, TG, and RC variability have been associated with several microvascular difficulties. Still, the pathogenic mechanism is not entirely known, and understanding how lipid variability affects microvascular disorders may lead to novel treatments. Furthermore, the current body of this research is restricted in its coverage. This field's lack of thorough investigations required a more extensive study and comprehensive effort. CONCLUSION: The relationship between lipid variation (LDL, HDL, and TG) (adverse effects) on microvascular complications, especially nephropathy and neuropathic (and maybe not retinopathy), is proven. Physicians and health policymakers should be highly vigilant to lipid variation in a general population.

Dynamic stability evaluation of trunk accelerations during walking in blind and sighted individuals.

BACKGROUND: Dynamic stability is a fundamental goal in standing activities. In this regard, monitoring, analysis, and interventions made to improve stability is a research topic investigated in the biomechanics of human movements. Vision has a major role to play in controlling human movement. Nonetheless, little is known about the effects of visual deprivation, especially from birth on dynamic gait stability. METHODS: The current study was conducted on 20 congenital blind and 10 sighted people (15-38 years). To evaluate the dynamic stability, descriptive data, harmonic ratio (HR), improved harmonic ratio (iHR), and root mean square (RMS), based on trunk acceleration data were measured in three axes: anteroposterior (AP), vertical (V), and mediolateral (ML) while participants walked an eight-meter straight path. RESULTS: In the comparison of blind and sighted people (eyes open), standard deviation, HR, iHR, and RMS indices were found to be significantly different in both AP and V directions. All the mentioned parameters were significantly lower in blind than in sighted participants. In the comparison of blind people and sighted ones with closed eyes, changes were observed in the maximum, range, standard deviation, and RMS only in the AP axis. In the comparison between eyes open and closed in sighted people, a significant difference was found only in the harmonic ratio of the vertical axis. CONCLUSION: Visual deprivation led to a decrease in dynamic stability parameters in the AP and V axes. Even the movement of sighted people in unchallenged conditions is dependent on visual information.

Prevalence of tobacco use among cancer patients in Iran: a systematic review and meta-analysis.

BACKGROUND: The prevalence of tobacco use among various cancer types in Iran remains a significant concern, necessitating a comprehensive analysis to understand the extent and patterns of consumption. This study aimed to systematically review and analyze existing literature to delineate the prevalence of tobacco use across different cancer types in Iran, thereby providing a robust basis for future interventions and policy formulations. METHODS: Adhering to the PRISMA guidelines, we conducted a systematic review and meta-analysis of literature available in PubMed and Scopus databases. The initial search identified 351 records, out of which 44 studies were selected based on their relevance and design. These studies spanned various time frames, starting from the 2001s up until 2022, and encompassed diverse geographical locations and cancer types in Iran. To avoid bias and potential data overlap, we opted to incorporate a single comprehensive study from the Golestan Cohort, encompassing all data, while excluding 10 other studies. Our final analysis incorporated data from 34 studies, which accounted for 15,425 patients and 5,890 reported smokers. Statistical analyses were performed to calculate the overall proportion of tobacco consumption and to conduct subgroup analyses based on different variables such as cancer types, gender, geographical locations, and types of tobacco used. RESULTS: The analysis revealed a substantial prevalence of tobacco use among cancer patients in Iran, with an overall consumption rate of 43%. This rate varied significantly, ranging from 10 to 88% across individual studies. Subgroup analyses further highlighted disparities in tobacco consumption rates across different demographics, geographic areas, and cancer types. Notably, the 'ever' smokers category exhibited the highest prevalence of tobacco use. The study also identified a worrying trend of high cigarette smoking rates, along with variable consumption patterns of other forms of tobacco, including waterpipe, 'Naas', and 'Pipe'. CONCLUSIONS: This systematic review and meta-analysis underscores a significant association between tobacco consumption and various cancer types in Iran, with a prevalence rate among cancer patients being three times higher than the average Iranian population. The findings indicate substantial heterogeneity in tobacco use patterns, emphasizing the need for targeted interventions to address this pressing health issue. The study serves as a critical resource for shaping future policies and strategies aimed at curbing tobacco use and mitigating its adverse effects on cancer prevalence in Iran.

Interactions of Fundamental Mie Modes with Thin Epsilon-near-Zero Substrates.

Extensive research has focused on Mie modes in dielectric nanoresonators, enabling the creation of thin optical devices surpassing their bulk counterparts. This study investigates the interactions between two fundamental Mie modes, electric and magnetic dipoles, and the epsilon-near-zero (ENZ) mode. Analytical, simulation, and experimental analyses reveal that the presence of the ENZ substrate significantly modifies these modes despite a large size mismatch. Electric and magnetic dipole modes, both with ∼12 THz line widths, exhibit 21 and 26 THz anticrossings, respectively, when coupled to the ENZ mode, indicating strong coupling. We also demonstrate that this strongly coupled system yields notably large subpicosecond nonlinear responses. Our results establish a solid foundation for designing functional, nonlinear, dynamic dielectric metasurfaces with ENZ materials.

RUNX1 Regulates a Transcription Program That Affects the Dynamics of Cell Cycle Entry of Naive Resting B Cells.

RUNX1 is a transcription factor that plays key roles in hematopoietic development and in hematopoiesis and lymphopoiesis. In this article, we report that RUNX1 regulates a gene expression program in naive mouse B cells that affects the dynamics of cell cycle entry in response to stimulation of the BCR. Conditional knockout of Runx1 in mouse resting B cells resulted in accelerated entry into S-phase after BCR engagement. Our results indicate that Runx1 regulates the cyclin D2 (Ccnd2) gene, the immediate early genes Fosl2, Atf3, and Egr2, and the Notch pathway gene Rbpj in mouse B cells, reducing the rate at which transcription of these genes increases after BCR stimulation. RUNX1 interacts with the chromatin remodeler SNF-2-related CREB-binding protein activator protein (SRCAP), recruiting it to promoter and enhancer regions of the Ccnd2 gene. BCR-mediated activation triggers switching between binding of RUNX1 and its paralog RUNX3 and between SRCAP and the switch/SNF remodeling complex member BRG1. Binding of BRG1 is increased at the Ccnd2 and Rbpj promoters in the Runx1 knockout cells after BCR stimulation. We also find that RUNX1 exerts positive or negative effects on a number of genes that affect the activation response of mouse resting B cells. These include Cd22 and Bank1, which act as negative regulators of the BCR, and the IFN receptor subunit gene Ifnar1 The hyperresponsiveness of the Runx1 knockout B cells to BCR stimulation and its role in regulating genes that are associated with immune regulation suggest that RUNX1 could be involved in regulating B cell tolerance.

Effect of sumac powder on clinical symptoms, hyperandrogenism, inflammation, blood glucose, lipid profiles in women with polycystic ovary syndrome: A double-blind randomized clinical trial.

Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders associated with a high risk of diabetes, atherosclerosis, and cardiovascular disease. The purpose of this study was to determine the effect of sumac powder on clinical symptoms and laboratory parameters in women with PCOS. The double-blind randomized controlled clinical trial was conducted on 88 women with PCOS randomly assigned to the intervention and control groups. The intervention group received three capsules each containing 1 g of sumac powder for 12 weeks. All data and serum levels of sex hormone, hs-CRP, glucose, and lipid profiles were measured at the baseline and at the end of the study. Data were analyzed using SPSS version 25 software. The ANCOVA test results showed that hs-CRP level was significantly reduced in the intervention group (p = .008). Blood glucose and lipid profiles in the intervention group were significantly reduced compared to the placebo group (p < .05). Insulin sensitivity and HDL levels were increased significantly in the Sumac group after the intervention (p < .05). Sumac powder can reduce the inflammatory effects, and glycemic status and lipid profile of polycystic ovaries in affected women, but has no significant effect on anthropometric parameters and sex hormones.

Evaluation of Mandibular Movements in Patients with Bell's Palsy Using Kinematic Variables.

Background: Since the function of muscles, and subsequently the mandibular joint, is affected in patients with Bell's palsy, therefore, the evaluation of facial muscles and mandibular function in these patients can be effective in diagnosis, prevention, and treatment planning. The present study aimed to evaluate the degree of displacement and range of motion (ROM) of the mandible and the ability of the facial symmetrical muscles of patients with Bell's palsy. Methods: This was a quasi-experimental comparative study. The variables evaluated were mandibular movement in a vertical direction and side-to-side displacement. Ten patients with Bell's palsy and 10 healthy eligible volunteers participated in the present study. Three mobile video cameras (to record jaw movements), 9 color markers, Kinovea software, House-Brackmann index, Toledo protocol, and a specialized patient questionnaire were used. Descriptive and inferential statistics were used for data analysis, the Kolmogorov-Smirnov test was used to investigate the normality of data distribution, and independent samples the t test and paired samples t test were used to compare means. Results: The maximum lateral on the sound side was 12.40 and 4.49 mm during lateral movements of the patients' mandible, while this value was between 12.30 and 3 mm on the involved side. There is a difference between the affected side and the nonaffected side in terms of the mean lateral movements of the patients' mandible. However, this difference in the mean ROM on both sides is not statistically significant. The maximum mouth opening in healthy individuals during mandibular movements was between 40 and 60 mm, while this value was between 25 and 50 mm in the patients with Bell's palsy. This study shows a significant difference (P = 0.007) between patients and healthy individuals in terms of the mean of maximum mouth opening ( P < 0.05). Conclusion: The results of this study showed that the ROM of temporomandibular joint (TMJ) of the patient is the same as that of normal subjects, but the side-to-side motion is more than normal which should be considered in rehabilitation treatments. The present study emphasizes the need to implement a mandibular kinematic evaluation protocol in patients with bell's palsy to prevent damage to the TMJ in the long term.

iNucs: inter-nucleosome interactions.

MOTIVATION: Deciphering nucleosome-nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS: We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. AVAILABILITYAND IMPLEMENTATION: https://github.com/Karimi-Lab/inucs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluating the efficacy of extracted squalene from seed oil in the form of microemulsion for the treatment of COVID-19: A clinical study.

This study investigates the effect of the nanostructure of squalene in the form of microemulsion on COVID-19 patients. In this blinded clinical trial, a comparison was made between the efficacy of squalene treatment and controls. A total of 30 COVID-19 patients admitted to the emergency department, and the infection ward was equally allocated to case (n = 15) and control (n = 15) groups according to their age and underlying diseases. The baseline characteristics of subjects, including age, gender, time of treatment onset, underlying condition, white blood cells count, and lymphocyte count were similar (p < 0.05). Baseline laboratory tests and computed tomography (CT) scans were performed for the study groups. The treatment group received 5 mg of intravenous squalene twice a day and standard treatment for 6 days, while controls received only standard treatment. After 6 days of treatment, clinical and CT scan changes were evaluated and compared in intervention and control groups. The need for oxygen therapy (p = 0.020), 2 days of no fever (p = 0.025), cough alleviation (p = 0.010), and lung high-resolution computed tomography improvement (p = 0.033) were significantly different between cases and controls within 7 days of admission. No adverse effects were observed in the treatment group. Our data suggest that squalene could be considered as a potential treatment for COVID-19, and further studies are required to confirm the results.

Altered Signatures of Plasma Inflammatory Proteins and Phonotypic Markers of NK Cells in Kidney Transplant Patients upon CMV Reactivation.

Cytomegalovirus (CMV) reactivation remains a common opportunistic infection with a prominent role in immune reconstitution in organ transplant recipients. CMVs as important drivers of natural killer (NK) cell differentiation has been indicated to prompt several phenotypic and functional alteration in these cells. We aimed to monitor the reconstitution of NK cells and change the signature of inflammatory proteins at the critical phase of CMV reactivation over six months after kidney transplantation. The present study indicated that CMV reactivation is associated with the development of IL-6, IL-10, and cytotoxic granules, including granzyme-B and granulysin, and the drop in the frequency of CD16 + NKG2A-CD57 + NK cell subset in kidney transplant recipients (KTRs) with reactivation versus non- reactivated ones. Our findings describe distinct immune signatures that emerged with CMV reactivation after kidney transplantation, which may be helpful in the timely management of CMV infection in KTRs.

Rolipram and pentoxifylline combination ameliorates experimental diabetic neuropathy through inhibition of oxidative stress and inflammatory pathways in the dorsal root ganglion neurons.

Diabetic neuropathy (DN) is the most challenging microvascular complication of diabetes and there is no suitable treatment for it, so the development of new agents to relieve DN is urgently needed. Since oxidative stress and inflammation play an essential role in the development of DN, clearance of these factors are good strategies for the treatment of this disease. According to key role of cyclic adenosine monophosphate (cAMP) in the regulation of oxidative stress and inflammatory pathways, it seems that phosphodiesterase inhibitors (PDEIs) can be as novel drug targets for improving DN through enhancement of cAMP level. The aim of this study was to evaluate the effects of rolipram, a selective PDE4 inhibitor, and pentoxifylline, a general PDE inhibitor on experimental model of DN and also to determine the possible mechanisms involved in the effectiveness of these agents. We investigated the effects of rolipram (1 mg/kg) and pentoxifylline (100 mg/kg) and also combination of rolipram (0.5 mg/kg) and pentoxifylline (50 mg/kg), orally for five weeks in rats that became diabetic by STZ (55 mg/kg, i.p.). After treatments, motor function was evaluated by open-field test, then rats were anesthetized and dorsal root ganglion (DRG) neurons isolated. Next, oxidative stress biomarkers and inflammatory factors were assessed by biochemical and ELISA methods, and RT-PCR analysis in DRG neurons. Rolipram and/or pentoxifylline treatment significantly attenuated DN - induced motor function deficiency by modulating distance moved and velocity. Rolipram and/or pentoxifylline treatment dramatically increased the cAMP level, as well as suppressed DN - induced oxidative stress which was associated with decrease in LPO and ROS and increase in TAC, total thiol, CAT and SOD in DRG neurons. On the other hand, the level of inflammatory factors (TNF-α, NF-kB and COX2) significantly decreased following rolipram and/or pentoxifylline administration. The maximum effectiveness was with rolipram and/or pentoxifylline combination on mentioned factors. These findings provide novel experimental evidence for further clinical investigations on rolipram and pentoxifylline combination for the treatment of DN.

Worldwide prevalence of microbial agents' coinfection among COVID-19 patients: A comprehensive updated systematic review and meta-analysis.

BACKGROUND: To provide information about pathogens' coinfection prevalence with SARS-CoV-2 could be a real help to save patients' lives. This study aims to evaluate the pathogens' coinfection prevalence among COVID-19 patients. METHOD: In order to find all of the relevant articles, we used systematic search approach. Research-based databases including PubMed, Web of Science, Embase, and Scopus, without language restrictions, were searched to identify the relevant bacterial, fungal, and viral coinfections among COVID-19 cases from December 1, 2019, to August 23, 2021. In order to dig deeper, other scientific repositories such as Medrxiv were probed. RESULTS: A total of 13,023 studies were found through systematic search. After thorough analysis, only 64 studies with 61,547 patients were included in the study. The most common causative agents of coinfection among COVID-19 patients were bacteria (pooled prevalence: 20.97%; 95% CI: 15.95-26.46; I2 : 99.9%) and less frequent were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31-18.96; I2 : 98.7%). The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84-17.36; I2 : 98.3%). Meta-regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity. CONCLUSION: We identified a high prevalence of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID-19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents' coinfection with SARS-CoV-2.

Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells.

Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at approximately embryonic day 15.5 (E15.5) in prospermatogonia. Earlier in germline development, the genome, including most retrotransposons, is progressively demethylated. Young ERVK and ERV1 elements, however, retain intermediate methylation levels. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, we determined whether retrotransposons are marked by H3K9me3 and H3K27me3 using a recently developed low-input ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) method. Although these repressive histone modifications are found predominantly on distinct genomic regions in E13.5 PGCs, they concurrently mark partially methylated long terminal repeats (LTRs) and LINE1 elements. Germline-specific conditional knockout of the H3K9 methyltransferase SETDB1 yields a decrease of both marks and DNA methylation at H3K9me3-enriched retrotransposon families. Strikingly, Setdb1 knockout E13.5 PGCs show concomitant derepression of many marked ERVs, including intracisternal A particle (IAP), ETn, and ERVK10C elements, and ERV-proximal genes, a subset in a sex-dependent manner. Furthermore, Setdb1 deficiency is associated with a reduced number of male E13.5 PGCs and postnatal hypogonadism in both sexes. Taken together, these observations reveal that SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline.

Conservative Treatment for Metatarsus Adductus, A Systematic Review of Literature.

There are various treatment approaches for the subjects with metatarsus adductus, including nonsurgical and surgical treatment. Nonsurgical treatments such as serial casting, modified shoes (Bebax shoe, Ipos antiadductus shoe) and orthoses (Wheaton brace, counter rotation system splint, Denis Brown bar, and Fillauer bar) are widely used in this regard. The main question posted here is which orthoses are more effective in correcting metatarsus adductus. Therefore, the aim of this review was to determine the efficiency of various nonsurgical treatments used for metatarsus adductus. MEDLINE/PubMed, EMBASE, Cochrane Central Register of Controlled Trial, Cochrane Data base of systematic review (CDSR), Scopus and ISI Web of knowledge (from 1960 to 2021) were searched by predefined search strategies to screen eligible randomized controlled studies meeting established criteria. The quality of the studies was assessed based on Down and Black tool. 200 studies on this topic were reviewed and finally 11 studies which met the inclusion criteria were selected for final analysis. These studies evaluated the efficiency of nonsurgical treatment options on foot angle and deformity correction in the subjects with metatarsus adductus. Quality of the papers based on Downs and Black tool varied between 13 and 23. Some treatments such as Wheaton brace, rigid strap, exercise (manipulation), reverse last shoe and plaster cast are used for these subjects. Although good correction can be achieved with use of these treatment methods, some of them have complications which should be considered in this regard. It seems that Wheaton brace and Bebax shoe have fewer complications compared to other methods.

Effects of exercise training on immunological factors in kidney transplant recipients; a randomized controlled trial.

The purpose of this study was to investigate the effects of a 12 week exercise training on the immune system of kidney transplant recipients. 23 kidney transplant recipients were randomly divided into two groups including control (n = 10) and training (n =13) groups. The training groups participated in the training for 10 weeks (three days a week; each day 60-90 minutes). The control group performed no regular exercise during this time. The blood samples were taken before and after 12 weeks. ELISA and Real-time PCR were used to evaluate cytokine profiles, including TNF-a, IL-6, IL-4, IL-31 and IL-35 as well as T-bet, GATA-3, RORYt and FOXP3, respectively. Finally, the data were analyzed, using paired T-test. ELISA results showed decreased levels of TNF- α, increased levels of IL-6 and no significant differences in the IL-35, IL-31 and IL-4 levels in the training group in comparison to the control group. Gene expression profiles showed significantly increased expression of T-bet and no changes in the GATA-3, RORYt and FOXP3 levels. According to these results, a moderate exercise including aerobic and resistance training could inhibit inflammatory cytokines and have beneficial effects on the immune system, but this issue needs further research.

The Effects of Lower Limb Orthoses on Health Aspects of the Spinal Cord Injury Patients: A Systematic Review Using International Classification of Functioning, Disability, and Health (ICF) as a Reference Framework.

Background: One of the most important approaches in the rehabilitation of spinal cord injury (SCI) patients is the use of different orthoses. To date, no review has been published that analyzed the effects of orthoses on health aspects of spinal cord injury clients using the International Classification of Functioning, Disability and Health (ICF). Methods: A systematic literature search was done in some databases, including Medline, PubMed, Cochrane centered register of the controlled trial (CCTR), Cochrane database of systematic reviews (CDSR), a database of abstracts of reviews of effects (DARE), Embase, Google Scholar, and ISI Web of Knowledge. SCI was used in conjunction with terms like orthotic device, mechanical orthoses, external power orthoses, assistive devices, and functional electrical. The time frame for this search was from 1970 to 2022. Results: A total of 200 papers were found. Based on the titles and abstracts, 100 related papers were detected. After careful evaluation of the papers, 47 studies were selected for final analysis-53 papers were excluded due to duplication, non-English language, and lack of full-text. Conclusion: The results of 32 studies (70% of studies) support the efficiency of orthoses in walking and standing of SCI patients. In most of the included studies, the efficiency of orthoses was evaluated mostly based on body functions and structures, and their impact on other outcomes such as participation and quality of life (QoL) of SCI patients was unclear.

Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3.

Genetic variation in the enzymes that catalyze posttranslational modification of proteins is a potentially important source of phenotypic variation during evolution. Ubiquitination is one such modification that affects turnover of virtually all of the proteins in the cell in addition to roles in signaling and epigenetic regulation. UBE2D3 is a promiscuous E2 enzyme, which acts as an ubiquitin donor for E3 ligases that catalyze ubiquitination of developmentally important proteins. We have used protein sequence comparison of UBE2D3 orthologs to identify a position in the C-terminal α-helical region of UBE2D3 that is occupied by a conserved serine in amniotes and by alanine in anamniote vertebrate and invertebrate lineages. Acquisition of the serine (S138) in the common ancestor to modern amniotes created a phosphorylation site for Aurora B. Phosphorylation of S138 disrupts the structure of UBE2D3 and reduces the level of the protein in mouse embryonic stem cells (ESCs). Substitution of S138 with the anamniote alanine (S138A) increases the level of UBE2D3 in ESCs as well as being a gain of function early embryonic lethal mutation in mice. When mutant S138A ESCs were differentiated into extraembryonic primitive endoderm, levels of the PDGFRα and FGFR1 receptor tyrosine kinases were reduced and primitive endoderm differentiation was compromised. Proximity ligation analysis showed increased interaction between UBE2D3 and the E3 ligase CBL and between CBL and the receptor tyrosine kinases. Our results identify a sequence change that altered the ubiquitination landscape at the base of the amniote lineage with potential effects on amniote biology and evolution.

H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2.

Phosphorylation of histone H3 at serine 10 (H3S10ph) by Aurora kinases plays an important role in mitosis; however, H3S10ph also marks regulatory regions of inducible genes in interphase mammalian cells, implicating mitosis-independent functions. Using the fluorescent ubiquitin-mediated cell cycle indicator (FUCCI), we found that 30% of the genome in interphase mouse embryonic stem cells (ESCs) is marked with H3S10ph. H3S10ph broadly demarcates gene-rich regions in G1 and is positively correlated with domains of early DNA replication timing (RT) but negatively correlated with H3K9me2 and lamin-associated domains (LADs). Consistent with mitosis-independent kinase activity, this pattern was preserved in ESCs treated with Hesperadin, a potent inhibitor of Aurora B/C kinases. Disruption of H3S10ph by expression of nonphosphorylatable H3.3S10A results in ectopic spreading of H3K9me2 into adjacent euchromatic regions, mimicking the phenotype observed in Drosophila JIL-1 kinase mutants. Conversely, interphase H3S10ph domains expand in Ehmt1 (also known as Glp) null ESCs, revealing that H3S10ph deposition is restricted by H3K9me2. Strikingly, spreading of H3S10ph at RT transition regions (TTRs) is accompanied by aberrant transcription initiation of genes co-oriented with the replication fork in Ehmt1-/- and Ehmt2-/- ESCs, indicating that establishment of repressive chromatin on the leading strand following DNA synthesis may depend upon these lysine methyltransferases. H3S10ph is also anti-correlated with H3K9me2 in interphase murine embryonic fibroblasts (MEFs) and is restricted to intragenic regions of actively transcribing genes by EHMT2. Taken together, these observations reveal that H3S10ph may play a general role in restricting the spreading of repressive chromatin in interphase mammalian cells.