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Abstract Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteomics. We introduce Spectralis, a de novo peptide sequencing method for tandem mass spectrometry. Spectralis leverages several innovations including a convolutional neural network layer connecting peaks in spectra spaced by amino acid masses, proposing fragment ion series classification as a pivotal task for de novo peptide sequencing, and a peptide-spectrum confidence score. On spectra for which database search provided a ground truth, Spectralis surpassed 40% sensitivity at 90% precision, nearly doubling state-of-the-art sensitivity. Application to unidentified spectra confirmed its superiority and showcased its applicability to variant calling. Altogether, these algorithmic innovations and the substantial sensitivity increase in the high-precision range constitute an important step toward broadly applicable peptide sequencing.

Brandon M Yanik,1 Jacqueline R Dauch,1 Hsinlin T Cheng1,2 1Department of Neurology, University of Michigan Medical Center, Ann Arbor, Michigan, USA; 2Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USACorrespondence: Hsinlin T ChengMassachusetts General Hospital, Harvard Medical School, WACC 835, 55 Fruit Street, Boston, MA 02114, USATel +1 2 617-724-6213Fax +1 2 617-724-0895Email htcheng@mgh.harvard.eduPurpose: Neurogenic inflammation is a major component of chronic neuropathic pain. Previously, we established the db/db mouse as an animal model of painful diabetic neuropathy (PDN) of type 2 diabetes. In the current study, we investigate the roles of interleukin (IL)-10, an anti-inflammatory cytokine, in the development of neurogenic inflammation and pain behavior in db/db mouse.Materials and Methods: We first studied IL-10 expression in lumbar dorsal root ganglion (LDRG) neurons of db/db mice using immunohistochemistry, immunoblots, and reverse transcription polymerase chain reaction during the period of pain behavior (from 8 to 16 wk of age). To determine if the reduced IL-10 expression mediates the mechanical allodynia in db/db mice, we administered recombinant mouse IL-10 or saline (control) intraperitoneally to control db/+ and db/db mice starting at 8 wk of age. IL-10 treatment was repeated every other day for 2 wk until the mice reached 10 wk of age.Results: During the period of pain behavior, reduction of IL-10 protein and gene expression was detected in LDRG of db/db mice. Treatment with recombinant IL-10, from 8 to 10 wk of age, alleviates pain behaviors in db/db mice without affecting other diabetic parameters. In parallel, IL-10 treatment reduced the upregulation of nerve growth factor (NGF), inducible nitric oxide synthase (iNOS), tumor necrosis factor (TNF)-α, and high-affinity NGF receptor (Trk A) in LDRG, as well as the numbers of iNOS-positive Langerhans cells and CD-68-positive dermal dendritic cells in the hind-foot-pad skin in db/db mice.Conclusion: Our findings suggest that the reduction in neuronal IL-10 increases inflammatory phenomena, ultimately contributing to PDN. These results suggest that the dysregulation of cytokine-mediated inflammation contributes to the development of PDN in db/db mice. Targeting this pathophysiologic mechanism could be an effective approach for treating PDN in type 2 diabetes.Keywords: dorsal root ganglion, painful diabetic neuropathy, cytokine, Langerhans cells, type 2 diabetes

What is expected from neuroprotection is to inhibit neuronal death and halt or decelerate the neuronal loss to lower the mortality rates, decrease disability, and improve the quality of life following an acute ischemic stroke. Several agents were described as neuroprotective up to date; however, there is still debate which to use in the neurorehabilitation of stroke patients, in terms of both efficacy and also safety. In this review, we discuss the agents, citicoline, cerebrolysin and MLC901 (NeuroAiD II), the three agents which have started to be used frequently in neurorehabilitation clinics recently in the light of the current literature., Competing Interests: Conflict of Interest: The authors declared no conflicts of interest with respect to the authorship and/or publication of this article., (Copyright © 2024, Turkish Society of Physical Medicine and Rehabilitation.)

Background: This descriptive analysis examines the victims of the February 6, 2023, earthquakes in Kahramanmaraş and Elbistan, Türkiye. It aims to detail the injury profiles related to neuro-musculoskeletal trauma, assess the rehabilitation needs of patients, and propose a comprehensive rehabilitation approach., Methods: The study included patients injured in the Kahramanmaraş-centered earthquake on February 6, 2023, who were transported to our hospital based on their rehabilitation needs. Data from patients treated at our hospital were recorded retrospectively. This included demographic information, accompanying pathologies, laboratory findings, rehabilitation programs, and treatments received during their hospital stay. Statistical analyses were conducted to examine the data., Results: A total of 141 patients with musculoskeletal injuries were admitted due to injuries sustained from the earthquake. The mean age of the participants was 39.76 years, with a slight female predominance (56.7%). The majority of patients sustained injuries while trapped under debris (90.1%), with an average duration of 10 hours under rubble. Fractures were the most common form of injury (53.2%), predominantly affecting the lower extremities. Peripheral nerve injuries were present in 41.1% of patients, and amputations were observed in 30.5%. Complications included compartment syndrome (46.1%), crush syndrome (36.2%), and various infections. Pain was prevalent among patients, with somatic pain being the most reported type. Individualized rehabilitation programs were implemented, incorporating physical therapy, wound care, pain management, and psychosocial support., Conclusion: This study highlights the critical rehabilitation needs of earthquake survivors and emphasizes the importance of early and comprehensive rehabilitation interventions. Multidisciplinary rehabilitation programs were crucial in addressing medical issues, functional limitations, and psychological challenges faced by the survivors. The findings contribute to a deeper understanding of earthquake-related injuries and underscore the significance of well-coordinated rehabilitation strategies in disaster responses.

Objective: The purpose of this study was to investigate the feasibility of the use of shear wave elastography (SWE) in comparison to chemical shift encoding (CSE) magnetic resonance imaging (MRI) for the evaluation of multifidus muscle fatty degeneration in patients with chronic low back pain., Method: Multifidus muscles were evaluated with the CSE-MRI and SWE examinations in control and patient groups. With the in-phase and out-phase sequences in CSE-MRI, signal intensity index (SII), and signal intensity suppression ratio (SISR) values; with the SWE method, shear wave velocity values were determined. Differences in the mean values of these parameters per level and study group were analyzed by Student's t-test., Results: SWE revealed significantly lower stiffness at the L2-3 level, consistent with the signal index values (SII-SISR) showing increased fatty infiltration on MRI in the patient group. No such relationship was found at the L4-5 level or in control group., Conclusions: SWE may be a promising method to show muscle fatty infiltration at L2-3 level in patients with chronic low back pain., (Copyright: © 2024 Permanyer.)

Objectives: The study aimed to examine the reasons for the rejection of manuscripts, considering the increased rejection rates of our journal of up to 73% in 2022, and help authors realize what the editors and referees are paying attention to while assessing the manuscript., Materials and Methods: In this retrospective study, original articles, case reports, systematic reviews, and meta-analyses submitted and rejected to the Turkish Journal of Physical Medicine Rehabilitation were searched between January 1, 2016, and June 30, 2022. After reviewing the referee's evaluations and editorial opinions for all rejected articles, the reasons for rejection were classified under three main headings: journal, manuscript, and ethical issues. The manuscript issues were detailed under 11 subheadings., Results: A total of 1,293 rejected submissions were reviewed. Of these, 35% were rejected at the editorial stage, while 65% were rejected after peer review. Thirty-three submissions were rejected for ethical reasons, 168 were out of the journal's field of interest, and 1,092 (84%) submissions were rejected for reasons related to the manuscript. The three most common reasons for rejection were protocol/methodology errors (44%), lack of contribution to the literature (41%), and lack of adequate discussion (40%)., Conclusion: Before starting the studies, supporting the hypotheses with the current literature review, planning with the right protocol, and interpreting the findings in the discussion will facilitate the acceptance of the manuscripts to our journal., Competing Interests: Conflict of Interest: The authors declared no conflicts of interest with respect to the authorship and/or publication of this article., (Copyright © 2023, Turkish Society of Physical Medicine and Rehabilitation.)

Objectives: This study aimed to investigate the physical and emotional effects of the coronavirus disease 2019 pandemic in patients with fibromyalgia syndrome (FMS) and chronic low back pain (CLBP) patients., Patients and Methods: The cross-sectional controlled study was performed with 1,360 participants (332 males, 1,028 females; mean age: 42.3±12.5 years; range, 18 to 65 years) between September 2020 and February 2021. The participants were evaluated in three groups: the FMS group (n=465), the CLBP group (n=455), and the healthy control group (n=440). Physical activity, pain levels, and general health status before and during the pandemic were evaluated in all participants. Stress levels were analyzed with the perceived stress scale (PSS) in all groups, and disease activity was analyzed with the fibromyalgia impact questionnaire (FIQ) in patients with FMS., Results: Patients with FMS had worsened general health status and pain levels during the pandemic compared to the other groups (p<0.01). The FMS group showed significantly higher PSS scores than those in other groups (p<0.01). There was a weak-positive correlation between FIQ and PSS parameters in patients with FMS (p<0.05, r=0.385)., Conclusion: The general health status, pain, and stress levels of the patients with FMS and CLBP tended to worsen during the pandemic. This high-stress level appeared to affect disease activity in patients with FMS., Competing Interests: Conflict of Interest: The authors declared no conflicts of interest with respect to the authorship and/or publication of this article., (Copyright © 2022, Turkish Society of Physical Medicine and Rehabilitation.)

Purpose The purpose of this study was to define posterior border distance (PBD), which represents an ultrasonographic diagnosing method of carpal tunnel syndrome (CTS), and to determine the reliability of PBD in comparison with electromyography (EMG) results. Methods Thirty-three patients (mean age: 51.8 ± 9.5 years; 27 females and six males) with CTS were included in this study. Ultrasonography (US) and EMG were performed under blinded conditions. PBD was evaluated by measuring the length of the perpendicular line between the posterior border of the median nerve and the line between the hook of the hamate and trapezoid tubercle. The cross-sectional area, anteroposterior (AP), and transverse diameter of the median nerve were measured. Control US was performed in 20 patients who were available at the first year postoperative follow-up and the results compared with preoperative US values. Correlation analyzes were performed to determine the relationship between electrodiagnostic results and ultrasonographic measurements. Results According to the results of preoperative and postoperative first-year US, there were statistically significant differences in the results of PBD (preoperative: 3.309±1.7472 mm, postoperative: 2.290±0.7867 mm p: 0.013) and AP diameter of the median nerve (preoperative: 3.012±0.7865 mm, postoperative: 2.680±0,5578 mm p: 0.017). There was no statistically significant difference in transverse diameter (preoperative: 6.585±1.9505 mm, postoperative: 6.955±2.2128 mm) and cross-sectional area (preoperative: 14.33±6.513 mm 2 , postoperative: 11.20±5.830 mm 2 ) results (p>0.05). The cut-off value of PBD was ≥3.6 mm, it yielded 81.48% specificity and 83.33% sensitivity in the diagnosis of CTS. PBD was correlated with motor and sensory latency, anteromedial, and transverse diameter of the median nerve (p<0.05). There was no correlation between EMG values and the results of the cross-sectional area, transverse diameter, and AP diameter of the median nerve (p>0.05). Conclusion PBD is suggested as a reliable ultrasonographic measurement method for the diagnosis of CTS., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2020, Meric et al.)