HLAncPred: a method for predicting promiscuous non-classical HLA binding sites.

Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional HLA-based immunotherapy, particularly against cancer and COVID-19 infection. In the last two decades, several methods have been developed to predict the binders of classical HLA alleles. In contrast, limited attempts have been made to develop methods for predicting non-classical HLA binding peptides, due to the scarcity of sufficient experimental data. Of note, in order to facilitate the scientific community, we have developed an artificial intelligence-based method for predicting binders of class-Ib HLA alleles. All the models were trained and tested on experimentally validated data obtained from the recent release of IEDB. The machine learning models achieved more than 0.98 AUC for HLA-G alleles on validation dataset. Similarly, our models achieved the highest AUC of 0.96 and 0.94 on the validation dataset for HLA-E*01:01 and HLA-E*01:03, respectively. We have summarized the models developed in the past for non-classical HLA and validated the performance with the models developed in this study. Moreover, to facilitate the community, we have utilized our tool for predicting the potential non-classical HLA binding peptides in the spike protein of different variants of virus causing COVID-19, including Omicron (B.1.1.529). One of the major challenges in the field of immunotherapy is to identify the promiscuous binders or antigenic regions that can bind to a large number of HLA alleles. To predict the promiscuous binders for the non-classical HLA alleles, we developed a web server HLAncPred (https://webs.iiitd.edu.in/raghava/hlancpred) and standalone package.

Comparison of instrumented and stand-alone lateral lumbar interbody fusion for lumbar degenerative disease: a systematic review and meta-analysis.

BACKGROUND: Both instrumented and stand-alone lateral lumbar interbody fusion (LLIF) have been widely used to treat lumbar degenerative disease. However, it remains controversial as whether posterior internal fixation is required when LLIF is performed. This meta-analysis aims to compare the radiographic and clinical results between instrumented and stand-alone LLIF. METHODS: PubMed, EMBASE and Cochrane Collaboration Library up to March 2023 were searched for studies that compared instrumented and stand-alone LLIF in the treatment of lumbar degenerative disease. The following outcomes were extracted for comparison: interbody fusion rate, cage subsidence rate, reoperation rate, restoration of disc height, segmental lordosis, lumbar lordosis, visual analog scale (VAS) scores of low-back and leg pain and Oswestry Disability Index (ODI) scores. RESULTS: 13 studies involving 1063 patients were included. The pooled results showed that instrumented LLIF had higher fusion rate (OR 2.09; 95% CI 1.16-3.75; P = 0.01), lower cage subsidence (OR 0.50; 95% CI 0.37-0.68; P < 0.001) and reoperation rate (OR 0.28; 95% CI 0.10-0.79; P = 0.02), and more restoration of disc height (MD 0.85; 95% CI 0.18-1.53; P = 0.01) than stand-alone LLIF. The ODI and VAS scores were similar between instrumented and stand-alone LLIF at the last follow-up. CONCLUSIONS: Based on this meta-analysis, instrumented LLIF is associated with higher rate of fusion, lower rate of cage subsidence and reoperation, and more restoration of disc height than stand-alone LLIF. For patients with high risk factors of cage subsidence, instrumented LLIF should be applied to reduce postoperative complications.

Laser Processing of Crumpled Porous Graphene/MXene Nanocomposites for a Standalone Gas Sensing System.

Integrating wearable gas sensors with energy harvesting and storage devices can create self-powered systems for continuous monitoring of gaseous molecules. However, the development is still limited by complex fabrication processes, poor stretchability, and sensitivity. Herein, we report the low-cost and scalable laser scribing of crumpled graphene/MXenes nanocomposite foams to combine stretchable self-charging power units with gas sensors for a fully integrated standalone gas sensing system. The crumpled nanocomposite designed in island-bridge device architecture allows the integrated self-charging unit to efficiently harvest kinetic energy from body movements into stable power with adjustable voltage/current outputs. Meanwhile, given the stretchable gas sensor with a large response of ∼1% ppm-1 and an ultralow detection limit of ∼5 ppb to NO2/NH3, the integrated system provides real-time monitoring of the exhaled human breath and the local air quality. The innovations in materials and structural designs pave the way for the future development of wearable electronics.

[Clinical outcomes of 3D-printing stand-alone artificial vertebral body in anterior cervical surgeries].

OBJECTIVE: To explore the short-term outcomes of 3D-printing stand-alone artificial vertebral body (AVB) in the surgical procedure of anterior cervical corpectomy and fusion (ACCF). METHODS: Following the proposal of IDEAL (idea, development, exploration, assessment, and long-term follow-up) framework, we designed and conducted this single-armed, retrospective cohort study. The patients with cervical spondylotic myelopathy were recruited, and these patients exclusively received the surgical procedure of single-level ACCF in our single center. After the process of corpectomy, the size was tailored using different trials and the most suitable stand-alone AVB was then implanted. This AVB was manufactured by the fashion of 3D-printing. Two pairs of screws were inserted in an inclined way into the adjacent vertebral bodies, to stabilize the AVB. The participants were regularly followed-up after the operation. Their clinical data were thoroughly reviewed. We assessed the neurological status according to Japanese Orthopedic Association (JOA) scale. We determined the fusion based on imaging examination six months after the operation. The recorded clinical data were analyzed using specific software and they presented in suitable styles. Paired t test was employed in comparison analysis. RESULTS: In total, there were eleven patients being recruited eventually. The patients were all followed up over six months after the operation. The mean age of the cohort was (57.2±10.2) years. The mean operation time was (76.1±23.1) min and the median bleeding volume was 150 (100, 200) mL. The postoperative course was uneventful for all the cases. Dysphagia, emergent hematoma, and deterioration of neurological function did not occur. Mean JOA scores were 13.2±2.2 before the operation and 16.3±0.8 at the final follow-up, which were significantly different (P < 0.001). The mean recovery rate of neurological function was 85.9%. By comparing the imaging examinations postoperatively and six months after the operation, we found that the average subsidence length was (1.2±1.1) mm, and that there was only one cases (9.1%) of the severe subsidence (>3 mm). We observed significant improvement of cervical lordosis after the operation (P=0.013). All the cases obtained solid fusion. CONCLUSION: 3D-printing stand-alone AVB presented favorable short-term outcome in one-level ACCF in this study. The fusion rate of this zero-profile prosthesis was satisfactory and the complication rate was relatively low.

A systematic review of anterior lumbar interbody fusion (ALIF) versus posterior lumbar interbody fusion (PLIF), transforaminal lumbar interbody fusion (TLIF), posterolateral lumbar fusion (PLF).

PURPOSE: The rate of elective lumbar fusion has continued to increase over the past two decades. However, there remains to be a consensus on the optimal fusion technique. This study aims to compare stand-alone anterior lumbar interbody fusion (ALIF) with posterior fusion techniques in patients with spondylolisthesis and degenerative disc disease through a systematic review and meta-analysis of the available literature. METHODS: A systematic review was performed by searching the Cochrane Register of Trials, MEDLINE, and EMBASE from inception to 2022. In the two-stage screening process, three reviewers independently reviewed titles and abstracts. The full-text reports of the remaining studies were then inspected for eligibility. Conflicts were resolved through consensus discussion. Two reviewers then extracted study data, assessed it for quality, and analysed it. RESULTS: After the initial search and removal of duplicate records, 16,435 studies were screened. Twenty-one eligible studies (3686 patients) were ultimately included, which compared stand-alone ALIF with posterior approaches such as posterior lumbar interbody fusion (PLIF), transforaminal lumbar interbody fusion (TLIF), and posterolateral lumbar fusion (PLF). A meta-analysis showed surgical time and blood loss was significantly lower in ALIF than in TLIF/PLIF, but not in those who underwent PLF (p = 0.08). The length of hospital stay was significantly shorter in ALIF than in TLIF, but not in PLIF or PLF. Fusion rates were similar between the ALIF and posterior approaches. The Visual Analogue Scale (VAS) scores for back and leg pain were not significantly different between the ALIF and PLIF/TLIF groups. However, VAS back pain favoured ALIF over PLF at one year (n = 21, MD - 1.00, CI - 1.47, - 0.53), and at two years (2 studies, n = 67, MD - 1.39, CI - 1.67, - 1.11). The VAS leg pain scores (n = 46, MD 0.50, CI 0.12 to 0.88) at two years significantly favoured PLF. The Oswestry Disability Index (ODI) scores at one year were not significantly different between ALIF and the posterior approaches. At two years, ODI scores were also similar between the ALIF and the TLIF/PLIF. However, the ODI scores at two years (2 studies, n = 67, MD - 7.59, CI - 13.33, - 1.85) significantly favoured ALIF over PLF (I2 = 70%). The Japanese Orthopaedic Association Score (JOAS) for low back pain at one year (n = 21, MD - 0.50, CI - 0.78) and two years (two studies, n = 67, MD - 0.36, CI - 0.65, - 0.07) significantly favoured ALIF over PLF. No significant differences were found in leg pain at the 2-year follow-up. Adverse events displayed no significant differences between the ALIF and posterior approaches. CONCLUSIONS: Stand-alone-ALIF demonstrated a shorter operative time and less blood loss than the PLIF/TLIF approach. Hospitalisation time is reduced with ALIF compared with TLIF. Patient-reported outcome measures were equivocal with PLIF or TLIF. VAS and JOAS, back pain, and ODI scores mainly favoured ALIF over PLF. Adverse events were equivocal between the ALIF and posterior fusion approaches.

Changes in psoas and posterior paraspinal muscle morphology after standalone lateral lumbar interbody fusion: a quantitative MRI-based analysis.

PURPOSE: Standalone lateral lumbar interbody fusion (SA-LLIF) without posterior instrumentation can be an alternative to 360° fusion in selected cases. This study aimed to investigate quantitative changes in psoas and paraspinal muscle morphology that occur on index levels after SA-LLIF. METHODS: Patients undergoing single- or multi-level SA-LLIF at L2/3 to L4/5 who had preoperative and postoperative lumbar MRI scans, the latter performed between 3 and 18 months after surgery for any reason, were retrospectively included. Muscle measurements were performed of the psoas and posterior paraspinal muscles (PPM; erector spinae and multifidus) on index levels using manual segmentation and an automated pixel intensity threshold method to differentiate muscle from fat signal. Changes in the total cross-sectional area (TCSA), the functional cross-sectional area (FCSA), and the percentage of fat infiltration (FI) of these muscles were assessed. RESULTS: A total of 67 patients (55.2% female, age 64.3 ± 10.6 years, BMI 26.9 ± 5.0 kg/m2) with 125 operated levels were included. Follow-up MRI scans were performed after an average of 8.7 ± 4.6 months, primarily for low back pain. Psoas muscle parameters did not change significantly, irrespective of the approach side. Among PPM parameters, the mean TCSA at L4/5 (+ 4.8 ± 12.4%; p = 0.013), and mean FI at L3/4 (+ 3.1 ± 6.5%; p = 0.002) and L4/5 (+ 3.0 ± 7.0%; p = 0.002) significantly increased. CONCLUSION: Our study demonstrated that SA-LLIF did not alter psoas muscle morphology, underlining its minimally invasive nature. However, FI of PPM significantly increased over time despite the lack of direct tissue damage to posterior structures, suggesting a pain-mediated response and/or the result of segmental immobilization.

Unraveling the complexities of Cd-aniline composite pollution: Insights from standalone and joint toxicity assessments in a bacterial community.

Cadmium (Cd) and aniline frequently co-occur in industrial settings but have rarely been addressed as composite toxicants in terms of the overall toxicity despite extensive knowledge of the environmental impact of each individual pollutant. In this study, we attempt to assess the relation of individual and combined toxic effects of Cd and aniline using a bacterial consortium cultured from soils as a model system. Results showed that the consortial bacteria exhibited drastically stronger tolerance to stand-alone Cd and aniline in comparison to literature data acquired from single species studies. When occurring simultaneously, the joint toxicity displayed a concentration-dependent behavior that wasn't anticipated based on individual chemical tests. Specifically, additive effects manifested with Cd and aniline at their IC10s, but changed to synergistic when the concentrations increased to IC20, and finally transitioned into antagonistic at IC30s and beyond. In addition, co-occurring aniline appeared to have retarded the cellular accumulation of Cd while increasing the enzymatic activities of superoxide dismutase and catalase relative to that in Cd-alone treatments. Finally, the bacterial community experienced distinct compositional changes under solo and combined toxicities with several genera exhibiting inconsistent behavior between treatments of single and composite toxicants. Findings from this study highlight the complexity of bacterial response to composite pollutions and point to the need for more comprehensive references in risk and toxicology assessment at multi-chemical contamination sites.

Unified Environment for Real Time Control of Hybrid Energy System Using Digital Twin and IoT Approach.

Today, climate change combined with the energy crisis is accelerating the worldwide adoption of renewable energies through incentive policies. However, due to their intermittent and unpredictable behavior, renewable energy sources need EMS (energy management systems) as well as storage infrastructure. In addition, their complexity requires the implementation of software and hardware means for data acquisition and optimization. The technologies used in these systems are constantly evolving but their current maturity level already makes it possible to design innovative approaches and tools for the operation of renewable energy systems. This work focuses on the use of Internet of Things (IoT) and Digital Twin (DT) technologies for standalone photovoltaic systems. Based on Energetic Macroscopic Representation (EMR) formalism and the Digital Twin (DT) paradigm, we propose a framework to improve energy management in real time. In this article, the digital twin is defined as the combination of the physical system and its digital model, communicating data bi-directionally. Additionally, the digital replica and IoT devices are coupled via MATLAB Simulink as a unified software environment. Experimental tests are carried out to validate the efficiency of the digital twin developed for an autonomous photovoltaic system demonstrator.

A Critical Review of Remote Sensing Approaches and Deep Learning Techniques in Archaeology.

To date, comprehensive reviews and discussions of the strengths and limitations of Remote Sensing (RS) standalone and combination approaches, and Deep Learning (DL)-based RS datasets in archaeology have been limited. The objective of this paper is, therefore, to review and critically discuss existing studies that have applied these advanced approaches in archaeology, with a specific focus on digital preservation and object detection. RS standalone approaches including range-based and image-based modelling (e.g., laser scanning and SfM photogrammetry) have several disadvantages in terms of spatial resolution, penetrations, textures, colours, and accuracy. These limitations have led some archaeological studies to fuse/integrate multiple RS datasets to overcome limitations and produce comparatively detailed outcomes. However, there are still knowledge gaps in examining the effectiveness of these RS approaches in enhancing the detection of archaeological remains/areas. Thus, this review paper is likely to deliver valuable comprehension for archaeological studies to fill knowledge gaps and further advance exploration of archaeological areas/features using RS along with DL approaches.

Immersive virtual reality for upper limb rehabilitation: comparing hand and controller interaction.

Virtual reality shows great potential as an alternative to traditional therapies for motor rehabilitation given its ability to immerse the user in engaging scenarios that abstract them from medical facilities and tedious rehabilitation exercises. This paper presents a virtual reality application that includes three serious games and that was developed for motor rehabilitation. It uses a standalone headset and the user's hands without the need for any controller for interaction. Interacting with an immersive virtual reality environment using only natural hand gestures involves an interaction that is similar to that of real life, which would be especially desirable for patients with motor problems. A study involving 28 participants (4 with motor problems) was carried out to compare two types of interaction (hands vs. controllers). All of the participants completed the exercises. No significant differences were found in the number of attempts necessary to complete the games using the two types of interaction. The group that used controllers required less time to complete the exercise. The performance outcomes were independent of the gender and age of the participants. The subjective assessment of the participants with motor problems was not significantly different from the rest of the participants. With regard to the interaction type, the participants mostly preferred the interaction using their hands (78.5%). All four participants with motor problems preferred the hand interaction. These results suggest that the interaction with the user's hands together with standalone headsets could improve motivation, be well accepted by motor rehabilitation patients, and help to complete exercise therapy at home.

Contemporary trends and in-hospital outcomes of catheter and stand-alone surgical ablation of atrial fibrillation.

AIMS: The contemporary trends in catheter ablation (CA) and surgical ablation (SA) utilization and surgical techniques [open vs. thoracoscopic, with or without left atrial appendage closure (LAAC)] are unclear. In addition, the in-hospital outcomes of stand-alone SA compared with CA are not well-described. METHODS AND RESULTS: The National Inpatient Sample 2010-18 was queried for atrial fibrillation (AF) hospitalizations with CA or stand-alone SA. Complex samples multivariable logistic and linear regression models were used to compare the association between stand-alone SA vs. CA and the primary outcomes of in-hospital mortality and stroke. Of 180 243 hospitalizations included within the study, 167 242 were for CA and 13 000 were for stand-alone SA. Catheter ablation and stand-alone SA hospitalizations decreased throughout the study period (Ptrend < 0.001). Surgical ablation had higher rates of in-hospital mortality [adjusted odds ratio (aOR) 2.26; 95% confidence interval (CI) 1.41-3.61; P = 0.001] and stroke (aOR 4.64; 95% CI 3.25-6.64; P < 0.001) compared with CA. When examining different surgical approaches, thoracoscopic SA was associated with similar in-hospital mortality (aOR 1.53; 95% CI 0.60-3.89; P = 0.369) and similar risk of stroke (aOR 1.75; 95% CI 1.00-3.07; P = 0.051) compared with CA. CONCLUSION: Stand-alone SA comprises a minority of AF ablation procedures and is associated with increased risk of mortality, stroke, and other in-hospital complications compared to CA. However, when a thoracoscopic approach was utilized, the risks of mortality and stroke appear to be reduced.

Reductions in particulate matter concentrations resulting from air filtration: A randomized sham-controlled crossover study.

One-hundred seventy-two households were recruited from regions with high outdoor air pollution (Fresno and Riverside, CA) to participate in a randomized, sham-controlled, cross-over study to determine the effectiveness of high-efficiency air filtration to reduce indoor particle exposures. In 129 households, stand-alone HEPA air cleaners were placed in a bedroom and in the main living area. In 43 households, high-efficiency MERV 16 filters were installed in central forced-air heating and cooling systems and the participating households were asked to run the system on a clean-air cycle for 15 min per hour. Participating households that completed the study received true air filtration for a year and sham air filtration for a year. Air pollution samples were collected at approximately 6-month intervals, with two measurements in each of the sham and true filtration periods. One week indoor and outdoor time-integrated samples were collected for measurement of PM2.5 , PM10 , and ultrafine particulate matter (UFP) measured as PM0.2 . Reflectance measurements were also made on the PM2.5 filters to estimate black carbon. True filtration significantly improved indoor air quality, with a 48% reduction in the geometric mean indoor PM0.2 and PM2.5 concentrations, and a 31% reduction in PM10 . Geometric mean concentrations of indoor/outdoor reflectance values, indicating fraction of particles of outdoor origin remaining indoors, decreased by 77%. Improvements in particle concentrations were greater with continuously operating stand-alone air cleaners than with intermittent central system filtration. Keeping windows closed and increased utilization of the filtration systems further improved indoor air quality.

Development of a decision-making pathway for utilizing standalone lateral lumbar interbody fusion.

PURPOSE: To develop a decision-making pathway for primary SA-LLIF. Furthermore, we analyzed the agreement of this pathway and compared outcomes of patients undergoing either SA-LLIF or 360-LLIF. METHOD: A decision-making pathway for SA-LLIF was created based on the results of interviews/surveys of senior spine surgeons with over 10 years of experience. Internal validity was retrospectively evaluated using consecutive patients undergoing either SA-LLIF or 360-LLIF between 01/2018 and 07/2020 with 3D-printed Titanium cages. An outcome assessment looking primarily at revision surgery and secondary at cage subsidence, changes in disk and foraminal height, global and segmental lumbar lordosis, duration of surgery, estimated blood loss, and length of stay was carried out. RESULTS: 78 patients with 124 treated levels (37 SA-LLIF, 41 360-LLIF) were retrospectively analyzed. The pathway showed a direct agreement (SA-LLIF) of 100.0% and an indirect agreement (360-LLIF) of 95.1%. Clinical follow-up averaged 13.5 ± 6.5 months including 4 revision surgeries in the 360-LLIF group and none in the SA-LLIF group (p = 0.117). Radiographic follow-up averaged 9.5 ± 4.3 months, with no statistically significant difference in cage subsidence rate between the groups (p = 0.440). Compared to preoperative images, patients in both groups showed statistically significant changes in disk height (p < 0.001), foraminal height (p < 0.001), as well as restoration of segmental lordosis (p < 0.001 and p = 0.018). The SA-LLIF group showed shorter duration of surgery, less estimated blood loss and shorter LOS (p < 0.001). CONCLUSION: The proposed decision-making pathway provides a guide to adequately select patients for SA-LLIF. Further studies are needed to assess the external applicability and validity. LEVEL OF EVIDENCE III: Diagnostic: individual cross-sectional studies with consistently applied reference standard and blinding.

Clinical and radiographic outcomes of stand-alone oblique lateral interbody fusion in the treatment of adult degenerative scoliosis: a retrospective observational study.

BACKGROUND: Open fusion and posterior instrumentation has traditionally been the treatment for adult degenerative scoliosis (ADS). However, minimally invasive treatment such as oblique lateral interbody fusion (OLIF) technique was developed as a new therapeutic method for the treatment of ADS. In addition, it is associated with decreased blood loss and shorter operative time without posterior instrument. The purpose of this study was to evaluate the efficiency of stand-alone OLIF for the treatment of ADS in terms of clinical and radiological results. METHODS: A total of 30 patients diagnosed with ADS who underwent stand-alone OLIF in our hospital from July 2017 to September 2018 were enrolled in the study. Scores from the Visual Analogue Scale (VAS) and Oswestry Disability Index (ODI) obtained preoperatively and at the final follow-up were compared. Radiography and computed tomography were performed preoperatively and at the final follow-up. The coronal cobb angle, lumbar lordosis, disc height, sacral slope, pelvic incidence and Pelvic tilt were recorded at each time point. RESULTS: The study cohort comprised 30 patients with a mean age of 64.5 ± 10.8 years and mean follow-up of 19.3 ± 4.2 months. The mean operative time was 96.8 ± 29.4 minutes and the mean estimated blood loss volume was 48.7 ± 9.4 ml. The mean coronal Cobb angle was corrected from 15.0° ± 3.7° preoperatively to 7.2° ± 3.1° postoperatively and 7.2° ± 3.3° at final follow-up (P < 0.0001). Lumbar lordosis significantly improved from 32.2° ± 11.3° preoperatively to 40.3° ± 11.8° postoperatively and 40.7° ± 11.0° at final follow-up (P < 0.01). The respective mean sacral slope and pelvic tilt improved from 26.1° ± 8.1° and 25.1° ± 6.9° preoperatively to 34.3° ± 7.4° and 19.2° ± 5.7° at final follow-up (P < 0.001). The mean disc height (defined as the mean of the anterior and posterior intervertebral disc heights) increased from 0.7 ± 0.3 cm preoperatively to 1.1 ± 0.2 cm at final follow-up (P < 0.0001). The interbody fusion rate on CT was 93.3%. The mean VAS pain score improved from 5.3 ± 0.6 before surgery to 2.3 ± 0.6 at final follow-up (P < 0.001). The mean ODI improved from 29.9% ± 6.8% preoperatively to 12.8% ± 2.4% at final follow-up (P < 0.001). CONCLUSIONS: Stand-alone OLIF is an effective and safe option for treating ADS in carefully selected patients. TRIAL REGISTRATION: The study was registered in the Chinese Clinical Trial Registry (ChiCTR2100052419).

Impact of cage position on biomechanical performance of stand-alone lateral lumbar interbody fusion: a finite element analysis.

BACKGROUND: This study aimed to compare the biomechanical performance of various cage positions in stand-alone lateral lumbar interbody fusion(SA LLIF). METHODS: An intact finite element model of the L3-L5 was reconstructed. The model was verified and analyzed. Through changing the position of the cage, SA LLIF was established in four directions: anterior placement(AP), middle placement(MP), posterior placement(PP), oblique placement(OP). A 400 N vertical axial pre-load was imposed on the superior surface of L3 and a 10 N/m moment was applied on the L3 superior surface along the radial direction to simulate movements of flexion, extension, lateral bending, and axial rotation. Various biomechanical parameters were evaluated for intact and implanted models in all loading conditions, including the range of motion (ROM) and maximum stress. RESULTS: In the SA LLIF models, the ROM of L4-5 was reduced by 84.21-89.03% in flexion, 72.64-82.26% in extension, 92.5-95.85% in right and left lateral bending, and 87.22-92.77% in right and left axial rotation, respectively. Meanwhile, ROM of L3-4 was mildly increased by an average of 9.6% in all motion directions. Almost all stress peaks were increased after SA LLIF, including adjacent disc, facet joints, and endplates. MP had lower stress peaks of cage and endplates in most motion modes. In terms of the stress on facet joints and disc of the cephalad segment, MP had the smallest increment. CONCLUSION: In our study, SA LLIF risked accelerating the adjacent segment degeneration. The cage position had an influence on the distribution of endplate stress and the magnitude of facet joint stress. Compared with other positions, MP had the slightest effect on the stress in the adjacent facet joints. Meanwhile, MP seems to play an important role in reducing the risk of cage subsidence.

Anterior cervical corpectomy and fusion with stand-alone cages in patients with multilevel degenerative cervical spine disease is safe.

BACKGROUND: In case of spinal cord compression behind the vertebral body, anterior cervical corpectomy and fusion (ACCF) proves to be a more feasible approach than cervical discectomy. The next step was the placement of an expandable titanium interbody in order to restore the vertebral height. The need for additional anterior plating with ACCF has been debatable and such technique has been evaluated by very few studies. The objective of the study is to evaluate radiographic and clinical outcomes in patients with multilevel degenerative cervical spine disease treated by stand-alone cages for anterior cervical corpectomy and fusion (ACCF). METHODS: Thirty-one patients (66.5 ± 9.75 years, range 53-85 years) were analyzed. Visual Analog Scale (VAS) and the 10-item Neck Disability Index (NDI) were assessed preoperatively and during follow-up on a regular basis after surgery and after one year at least. Assessment of radiographic fusion, subsidence, and lordosis measurement of Global cervical lordosis (GCL); fusion site lordosis (FSL); the anterior interbody space height (ant. DSH); the posterior interbody space height (post. DSH); the distance of the cage to the posterior wall of the vertebral body (CD) were done retrospectively. Mean clinical and radiographic follow-up was 20.0 ± 4.39 months. RESULTS: VAS-neck (p = 0.001) and VAS-arm (p < 0.001) improved from preoperatively to postoperatively. The NDI improved at the final follow-up (p < 0.001). Neither significant subsidence of the cages nor significant loss of lordotic correction were seen. All patients showed a radiographic union of the surgically addressed segments at the last follow up. CONCLUSIONS: Application of a stand-alone expandable cage in the cervical spine after one or two-level ACCF without additional posterior fixation or anterior plating is a safe procedure that results in fusion. Neither significant subsidence of the cages nor significant loss of lordotic correction were seen. TRIAL REGISTRATION: Retrospectively registered. According to the Decision of the ethics committee, Jena on 25th of July 2018, that this study doesn't need any registration.  https://www.laek-thueringen.de/aerzte/ethikkommission/registrierung/ .

Standalone cage versus anchored cage for anterior cervical discectomy and fusion: a comparative analysis of clinical and radiological outcomes.

PURPOSE: The use of standalone cages (SAC) and anchored cages (AC) in anterior cervical discectomy and fusion surgery (ACDF) has shown advantage of reduced operative time and lower incidence of dysphagia. However, there is limited literature available comparing the clinical and radiological outcomes of SAC and AC. METHODS: We conducted a prospective study for patients undergoing ACDF for cervical radiculopathy or myelopathy. Patient were classified based on the cage used into SAC group and the AC group. Clinical outcomes were assessed using the modified Japanese Orthopedic Association (mJOA) for myelopathy and Neck Disability Index (NDI) and Visual Analogue Scale (VAS) for radiculopathy. Dysphagia was graded as per Bazaz score. Radiologically, global cervical lordosis, segmental lordosis, cage subsidence, and migration were assessed. RESULTS: We analyzed 31 patients in each group with a minimum two year follow-up. The mean VAS improved from 7.9 to 4.56, mean NDI score improved from 27.6 to 19.8, and mean mJOA improved from 10.8 to 11.7 which were statistically significant (p < 0.05); however, no significant difference was noted between the SAC and AC groups. Mean global lordosis improved from 14.4 to 20.3° and mean segmental lordosis improved from 6 to 10.1° at six months and plateaued to 6.9° at final follow up without any significant difference between the groups. The subsidence was statistically more in 12.9% (4/31) in SAC than 6.4% (2/31) in AC. CONCLUSION: AC showed of lower rates of subsidence while both SAC and AC had comparable clinical outcomes and radiological alignment outcomes.

GENPPI: standalone software for creating protein interaction networks from genomes.

BACKGROUND: Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results. RESULTS: We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 min on a conventional computer. Moreover, the interaction networks that our software creates reflect correct evolutionary relationships between species, which we confirmed with average nucleotide identity analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice regarding which set of genomes they are going to study. CONCLUSIONS: GENPPI can help fill the gap concerning the considerable number of novel genomes assembled monthly and our ability to process interaction networks considering the noncore genes for all completed genome versions. With GENPPI, a user dictates how many and how evolutionarily correlated the genomes answer a scientific query.

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis.

BACKGROUND: RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. RESULTS: Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. CONCLUSIONS: RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software.

ePharmer: An integrated and graphical software for pharmacophore-based virtual screening.

Pharmacophore-based virtual screening (VS) has emerged as an efficient computer-aided drug design technique when appraising multiple ligands with similar structures or targets with unknown crystal structures. Current pharmacophore modeling and analysis software suffers from inadequate integration of mainstream methods and insufficient user-friendly program interface. In this study, we propose a stand-alone, integrated, graphical software for pharmacophore-based VS, termed ePharmer. Both ligand-based and structure-based pharmacophore generation methods were integrated into a compact architecture. Fine-grained modules were carefully organized into the computing, integration, and visualization layers. Graphical design covered the global user interface and specific user operations including editing, evaluation, and task management. Metabolites prediction analysis with the chosen VS result is provided for preselection of wet experiments. Moreover, the underlying computing units largely adopted the preliminary work of our research team. The presented software is currently in client use and will be released for both professional and nonexpert users. Experimental results verified the favorable computing capability, user convenience, and case performance of the proposed software.