ModiFinder: Tandem Mass Spectral Alignment Enables Structural Modification Site Localization.

Untargeted tandem mass spectrometry (MS/MS) has become a high-throughput method to measure small molecules in complex samples. One key goal is the transformation of these MS/MS spectra into chemical structures. Computational techniques such as MS/MS library search have enabled the reidentification of known compounds. Analog library search and molecular networking extend this identification to unknown compounds. While there have been advancements in metrics for the similarity of MS/MS spectra of structurally similar compounds, there is still a lack of automated methods to provide site specific information about structural modifications. Here we introduce ModiFinder which leverages the alignment of peaks in MS/MS spectra between structurally related known and unknown small molecules. Specifically, ModiFinder focuses on shifted MS/MS fragment peaks in the MS/MS alignment. These shifted peaks putatively represent substructures of the known molecule that contain the site of the modification. ModiFinder synthesizes this information together and scores the likelihood for each atom in the known molecule to be the modification site. We demonstrate in this manuscript how ModiFinder can effectively localize modifications which extends the capabilities of MS/MS analog searching and molecular networking to accelerate the discovery of novel compounds.

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention.

Identifying and discovering druggable protein binding sites is an important early step in computer-aided drug discovery, but it remains a difficult task where most campaigns rely on a priori knowledge of binding sites from experiments. Here, we present a binding site prediction method called Graph Attention Site Prediction (GrASP) and re-evaluate assumptions in nearly every step in the site prediction workflow from data set preparation to model evaluation. GrASP is able to achieve state-of-the-art performance at recovering binding sites in PDB structures while maintaining a high degree of precision which will minimize wasted computation in downstream tasks such as docking and free energy perturbation.

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention.

Identifying and discovering druggable protein binding sites is an important early step in computer-aided drug discovery but remains a difficult task where most campaigns rely on a priori knowledge of binding sites from experiments. Here we present a novel binding site prediction method called Graph Attention Site Prediction (GrASP) and re-evaluate assumptions in nearly every step in the site prediction workflow from dataset preparation to model evaluation. GrASP is able to achieve state-of-the-art performance at recovering binding sites in PDB structures while maintaining a high degree of precision which will minimize wasted computation in downstream tasks such as docking and free energy perturbation.

Significant slope reduction in ACL deficiency can be achieved both by anterior closing-wedge and medial open-wedge high tibial osteotomies: early experiences in 76 cases.

PURPOSE: It has been proven that a steep tibial slope (TS) is a risk factor for anterior cruciate ligament (ACL) injury and graft insufficiency after ACL reconstruction (ACLR). Recently, there is an increasing number of case series on slope decreasing osteotomies after failed ACLR utilizing different techniques and strategies. Goal of the present study is to report on early experiences with slope decreasing osteotomies in ACL deficient knees with special emphasis on the amount of slope correction, technical details, and complications; and to further analyze differences of slope corrections between sole sagittal as well as combined coronal and sagittal realignment procedures. In addition, we wanted to study if sole sagittal corrections change the coronal alignment. METHODS: Seventy-six patients with a minimum follow-up of 6 months were identified, who underwent a sole sagittal correction (anterior closed-wedge high tibial osteotomy (ACW-HTO)) or a combined procedure with an additional coronal realignment (medial open-wedge high tibial osteotomy (MOW-HTO)). In ACW-HTO, either infratuberosity or supratuberosity approaches were used. The medial TS was measured on lateral radiographs and the anatomical medial proximal tibial angle (aMPTA) was measured on anterior-posterior radiographs. Technical details and specific complications were recorded. RESULTS: Fifty-eight ACW-HTO and 18 MOW-HTO were performed. Regarding ACW-HTO, an infratuberosity (N = 48) or a supratuberosity (N = 10) approach was chosen. Sixty-seven patients had at least 1 previous ACLR. Mean TS changed from 14.5 ± 2.2° to 6.8 ± 1.9° (P < 0.0001). Mean TS of ACW-HTO was significantly reduced (14.6 ± 2.3° vs. 6.5 ± 1.9°; P < 0.0001), whereas in combined coronal and sagittal realignments, from 14.1 ± 1.9° to 7.6 ± 1.9° (P < 0.0001). The TS reduction in sole sagittal corrections was significantly higher compared to combined procedures (8.1 ± 1.6 vs. 6.4 ± 1.6°; P = 0.0002). Mean aMPTA in ACW-HTO changed from 87.1 ± 2.1° to 87.4 ± 2.8 (n.s.). However, there was a significant inverse correlation between the amount of sagittal correction and coronal alteration (r = - 0.29; P = 0.028). There was one late implant infection, which occurred 5.5 months after the index surgery. CONCLUSIONS: ACW-HTO and MOW-HTO facilitate significant slope reduction with a low-risk profile in patients with ACL insufficiency and a high tibial slope. AOW-HTO does not significantly alter coronal alignment in the majority of patients. LEVEL OF EVIDENCE: IV.

The Posterolateral Instability Score (PoLIS) of the knee joint: a guideline for standardized documentation, classification, and surgical decision-making.

PURPOSE: There has been a recent resurgence in interest in posterolateral instabilities of the knee joint. As this terminology comprises a large variety of pathologies, confusion and ambiguity in communication between surgeons and allied health professionals are generated. Consequently, accurate classification criteria are required to account for thorough preoperative diagnostics, surgical decision-making, and a standardized scientific documentation of injury severity. METHODS: A working group of five knee surgeons, who retrospect more than 2000 reconstructions of the posterolateral corner (PLC) at the minimum, was founded. An advanced PubMed search was conducted to identify key definitions. After defining an accurate diagnostic work-up, popular consensus was reached on definitions and covariates for a novel classification, rating of injury severity, and the resulting surgical decision-making. RESULTS: Three columns (lateral instability, cruciate ligament involvement, and relevant covariates), each ranging from A to D with increasing severity and assigning a number of points, were needed to meet the requirements. The generated terminology translated into the Posterolateral Instability Score (PoLIS) and the added number of points, ranging from 1 to 18, depicted the injury severity score. CONCLUSION: The presented classification may enable an objective assessment and documentation of the injury severity of the inherently complex pathology of injuries to the lateral side of the knee joint. LEVEL OF EVIDENCE: V.

Tibial Slope Correction as an Infratuberosity Closing-Wedge Extension Osteotomy in ACL-Deficient Knees. / Die tibiale Slope-Korrektur als infratuberositär zuklappende Extensionsosteotomie bei Insuffizienz des vorderen Kreuzbandes.

ACL insufficiency can be caused by different reasons. Elevated posterior tibial slope is a deformity which is discussed to have relevant influence on the outcome of ACL surgery. A increased posterior tibial slope of 12° or more leads to significant more ACL insufficiency. The surgical therapy of this pathology is a high tibial extension osteotomy. Publications ashowing a clinical follow up and results of this surgery are rare. In this video the technique of a closed wedge high tibial extension osteotomy is shown. Osteosynthesis is performed with two screws and an anklestable plate osteosynthesis. An arthroscopy with bone graft filling of the femoral ACL tunnel is performed first, followed by filling of the tibial tunnel in an open approach.

Isolated AL bundle reconstruction of the PCL.

INTRODUCTION: The purpose of this study was to evaluate the clinical and radiologic results after isolated reconstruction of the posterior cruciate ligament (PCL) using the semitendinosus (ST) and gracilis (GR) tendons with the arthroscopic single-bundle technique. METHODS: All patients upon whom we had performed a single-bundle PCL reconstruction between 2002 and 2005 prospectively underwent a standardized follow-up examination after 2 years. Isolated PCL reconstruction was carried out on 41 patients during the observation period. Pre- and postoperative stress radiographs were taken using the Telos stress device in order to evaluate the dorsal translation. Knee joint function and degree of activity were recorded using the Tegner activity score, the subjective International Knee Documentation Committee (IKDC) score, and the overall IKDC score. RESULTS: 33 of 41 patients (80.4%, 17 men, 16 women) completed the study. The posterior tibial translation of -10.1 ± 1.8 mm had an overall average improvement to a postoperative value of -5.0 ± 2.5 mm (p < 0.001). The patients showed a significant improvement in the Tegner activity score from an average 2.8 ± 0.8 points to 5.9 ± 1.2 points (p < 0.001). Evaluation of the subjective IKDC showed a significant improvement from a preoperative score of 41.86 ± 11.49 points to a postoperative score of 69.54 ± 11.39 points (p < 0.001). In total, 24 patients (72.8%) exhibited a normal or nearly normal outcome. CONCLUSION: The abovementioned reconstruction technique can achieve a stable knee function in patients with isolated PCL insufficiency. The isolated single-bundle PCL reconstruction offers an improvement regarding the activity level and stability of the knee joint. LEVEL OF EVIDENCE: Level IV.

Distribution of posterior tibial displacement in knees with posterior cruciate ligament tears.

BACKGROUND: While stress radiography has been used to objectively determine the limits of posterior tibial displacement in knees with posterior cruciate ligament tears, the magnitude and distribution of posterior tibial translation has not been defined in a large population of patients with this injury. METHODS: A retrospective diagnostic study of 1041 consecutive patients with posterior cruciate ligament tears was done. Posterior tibial displacement values that were obtained with use of instrumented stress radiography with the knee held in 90 degrees of flexion in the Telos device were evaluated and compared with the values from relevant cadaveric dissection studies. RESULTS: The mean amount of posterior tibial displacement on stress radiographs was -11.58 +/- 4.31 mm (range, -5 to -30 mm). There was a displacement peak in the range of -9 to -12 mm, with 37.9% of patients exhibiting posterior laxity within this range. Traffic-related injuries were associated with significantly greater displacement values than were sports-related injuries (p < 0.001). Grade-I or II instability (12 mm of posterior tibial displacement) occurred in association with 68.7% of the sports-related injuries, compared with 54.1% of the traffic-related injuries (p < 0.001). The mean amount of posterior tibial displacement on the intact side was -1.31 +/- 1.85 mm (range, -6 to 4 mm). CONCLUSIONS: Instrumented stress radiography is a useful testing method for objectively determining the amount of posterior tibial displacement of the knee in adults with a posterior cruciate ligament injury. Absolute posterior tibial displacement in excess of 8 mm is indicative of complete insufficiency of the posterior cruciate ligament. With tibial displacement exceeding 12 mm, additional injury of secondary restraining structures should be considered. We recommend the use of stress radiography to grade and classify posterior knee laxity.

Initial fixation strength of a new hybrid technique for femoral ACL graft fixation: the bone wedge technique.

BACKGROUND: Aperture fixation with interference screws matching the diameter of the tunnel is associated with the risk of graft laceration and graft rotation. HYPOTHESIS: A hybrid fixation technique (extracortical and aperture fixation) with undersized interference screw placed behind a bone wedge provides a higher fixation strength as aperture fixation with a screw alone matching the size of the tunnel. STUDY DESIGN: Experimental laboratory study. METHODS: We evaluated the initial fixation strength (single cycle and cyclic loading tests) of hybrid and interference screw aperture fixation using different sized interference screws in porcine knees. RESULTS: Analysis of yield load, maximum load and stiffness in the single cycle loading test showed no statistically significant differences for hybrid fixation with a 1 mm undersized screw and aperture fixation with a screw matching the size of the tunnel. The use of an undersized screw alone resulted in low fixation strength. CONCLUSION: The initial fixation strength of the hybrid technique with undersized screws is comparable to that of interference screw fixation matching the size. CLINICAL RELEVANCE: The new "bone wedge fixation" is an alternative for ACL graft fixation without the risk of graft laceration and graft rotation.

Initial fixation strength of a hybrid technique for femoral ACL graft fixation.

Aperture fixation with interference screws matching the diameter of the tunnel is associated with the risk of graft laceration and graft rotation. A hybrid fixation technique (extracortical and aperture fixation) with undersized interference screws provides a higher fixation strength when compared to an aperture fixation using only a screw matching the size of the tunnel and also reduces the risk of graft laceration. This research is an experimental laboratory study. We evaluated the initial fixation strength at time-zero of an extracortical-, a hybrid- and an aperture fixation in ACL reconstruction using extracortical buttons and different sized interference screws in porcine knees. The tests were performed using a single cycle and cyclic loading protocol. Analysis of yield load, maximum load and stiffness in the single cycle loading test showed no statistically significant differences for hybrid fixation with a 1 mm undersized screw and aperture fixation with a screw matching the size of the tunnel. Cyclic loading tests showed a statistically significant difference between hybrid and aperture fixation. The use of an undersized screw alone in aperture fixation resulted in insufficient fixation strength. The initial fixation strength of the hybrid technique with undersized screws is higher compared to an interference screw fixation alone. The hybrid fixation technique is an alternative for ACL graft fixation.

Combined anterior cruciate ligament, posterior cruciate ligament, and posterolateral corner reconstruction with autogenous hamstring grafts in chronic instabilities.

PURPOSE: The purpose of this study was to evaluate the clinical outcome after 1-stage reconstructions of the anterior and posterior cruciate ligaments (ACL, PCL) with reconstruction of the posterolateral corner (PLC) structures using autogenous hamstring grafts in chronic knee injuries. TYPE OF STUDY: Prospective case series. METHODS: We reviewed 17 patients (13 men and 4 women) with chronic multiligamentous injuries after a minimum follow-up of 2 years (range, 24 to 66.3 months). Arthroscopically assisted combined ACL/PCL reconstructions with autogenous semitendinosus-gracilis tendon grafts were performed using the single-incision endoscopic ACL technique and the single femoral tunnel, single-bundle transtibial tunnel PCL technique. The PLC was reconstructed with a free autogenous semitendinous tendon graft. The primary outcome measures were the International Knee Documentation Committee (IKDC) score and stress radiography. As secondary outcome measure, all patients were evaluated with a subjective questionnaire, physical examination, radiologic assessment, and KT-1000 arthrometer testing. RESULTS: The mean time from injury to the reconstructive procedure was 70.2 +/- 96.7 months (range, 5.1 to 312.6 months). At final IKDC evaluation, 4 patients (29.4%) were graded level B (nearly normal), 10 patients (58.8%) level C (abnormal), and 2 patients (11.8%) level D (grossly abnormal). The mean postoperative subjective IKDC score was 71.8 +/- 19.3 points. Mean posterior tibial displacement as measured through stress radiography at 90 degrees of knee flexion was reduced from -15.06 +/- 4.68 mm preoperatively to -7.12 +/- 3.37 mm postoperatively (P < .001). Mean anterior tibial displacement was 0.94 +/- 2.75 mm preoperatively compared with -1.59 +/- 3.50 mm postoperatively (P < .01). Three patients had a fixed posterior tibial subluxation (posterior tibial displacement < or = -3 mm on anterior stress radiographs) postoperatively. Severe subjective instability was reduced significantly by the operative procedure (P < .001). The mean postoperative total anterior-posterior side-to-side difference with the KT-1000 arthrometer testing was 2.00 +/- 2.23 mm (range, -4 to 7 mm). CONCLUSIONS: Combined chronic ACL/PCL/PLC instabilities can be successfully treated with 1-stage arthroscopic cruciate ligament reconstruction combined with PLC reconstruction using autogenous hamstring grafts. Although current reconstruction techniques are not able to restore normal tibiofemoral kinematics, most patients recover a functionally stable knee and have considerably improved knee function compared with their preoperative status, based on subjective parameters and objective criteria. LEVEL OF EVIDENCE: Level IV, case series, no historical or control group.

Joint kinematics and in situ forces after single bundle PCL reconstruction: a graft placed at the center of the femoral attachment does not restore normal posterior laxity.

INTRODUCTION: Femoral tunnel placement has a great influence on the clinical outcome after PCL reconstruction. MATERIALS AND METHODS: Using a robotic/universal force moment sensor (UFS) testing system, we examined joint kinematics and in situ forces of human knees following soft-tissue single bundle PCL reconstruction fixed at the center of the femoral attachment. RESULTS: Posterior tibial translation significantly increased at all flexion angles after transsection of the posterior cruciate ligament (p<0.05). PCL reconstruction resulted in significantly less posterior tibial translation at all flexion angles when compared to the PCL deficient knee (p<0.05). The differences in the in situ force between the intact ligament and the reconstructed graft were statistical significant (p<0.05). CONCLUSION: Single bundle PCL reconstruction with a soft-tissue graft fixed at the center of the femoral attachment is able to reduce the posterior tibial translation significantly. However, it cannot restore kinematics of the intact knee and in situ forces of the intact PCL.

Importance of femoral tunnel placement in double-bundle posterior cruciate ligament reconstruction: biomechanical analysis using a robotic/universal force-moment sensor testing system.

BACKGROUND: Previous studies have identified the femoral attachment of the posterior cruciate ligament fibers as one of the primary determinants of fiber tension behavior. In addition, a double-bundle posterior cruciate ligament reconstruction has been shown to restore the intact knee kinematics more closely than does a single-bundle reconstruction. HYPOTHESIS: An anterior tunnel position in double-bundle posterior cruciate ligament reconstruction restores the biomechanics of the normal knee more closely than does a posterior tunnel position. STUDY DESIGN: Controlled laboratory study. METHODS: Kinematics and in situ forces of human knees after double-bundle posterior cruciate ligament reconstruction with 2 different femoral tunnel positions (anterior vs posterior) were evaluated using a robotic/universal force-moment sensor testing system. Within the same specimen, the resulting knee kinematics and in situ forces were compared. For statistical analysis, 2-way analysis of variance repeated measures were performed. RESULTS: The femoral tunnel position of the double-bundle hamstring graft had significant effect on the resulting posterior tibial displacement and in situ forces of the hamstring grafts. The anterior femoral tunnel position provided significantly less posterior tibial translation than did the posterior tunnel position. There was a tendency toward higher in situ forces of grafts fixed in the anterior tunnel when compared to the posterior position, but this difference was statistically not significant. CONCLUSION: An anterior position of the bone tunnels in double-bundle posterior cruciate ligament reconstruction restores the normal knee kinematics more closely than does a posterior position of the tunnels. CLINICAL RELEVANCE: In double-bundle posterior cruciate ligament reconstruction, posterior placement of the tunnel should be avoided.

Development of a perforated biodegradable interference screw.

PURPOSE: The objective was to develop a perforated biodegradable interference screw to allow for enhanced osseous implant integration without impairing screw stability during insertion. TYPE OF STUDY: Mechanical testing, followed by animal study. METHODS: At first, manual perforation of 8 x 23-mm biodegradable poly-(L-co-D,L-lactide) interference screws was performed, using 3 different perforation patterns (clockwise spiral, counter-clockwise spiral, and parallel perforation), followed by torsional tests. Next, parallel perforated screws (n = 6) and unperforated control screws (n = 6) were applied to the proximal tibia of 12 sheep. The sheep were put down after 24 weeks and the screw site was examined histologically. Subsequently, molding of a parallel perforated screw followed by torsional tests was undertaken. RESULTS: The parallel perforated screw presented a torsional strength insignificantly different from the unperforated control screw and well beyond the reported maximum manual insertion torques of biodegradable interference screws in young human bone. When compared with the regular unperforated interference screw, the molded perforated screw exhibited a torsional strength of 91%, indicating a secure surgical application. In contrast to the unperforated screw, histologic evaluations revealed clear bone ingrowth into the perforations including the core of the perforated interference screw. CONCLUSIONS: Perforated, "cage-like" interference screws may be promising for the acceleration of osseous implant integration into the bone with a very low risk of screw breakage during insertion. CLINICAL RELEVANCE: To ameliorate osseous implant integration and possibly enhance ossification of former implant site in anterior cruciate ligament surgery.

Reliability of stress radiography for evaluation of posterior knee laxity.

BACKGROUND: Although stress radiography has been recommended for quantifying posterior tibial displacement in knees with posterior cruciate ligament insufficiency, the intratester reliability and intertester reliability of this measurement method have not been evaluated. HYPOTHESIS: Stress radiography is a reproducible measurement method in the assessment of posterior knee laxity in patients with posterior cruciate ligament lesions. STUDY DESIGN: Cohort study (diagnosis); Level of evidence, 2. METHODS: Stress radiographs of 787 patients with suspected posterior cruciate ligament lesions taken using the Telos device were evaluated independently by 3 testers: 2 of the testers were clinically experienced in the evaluation of stress radiographs, and 1 tester was a novice tester. Change in mean, standard error of measurement with calculated confidence intervals, and intra-class correlation coefficients were determined to assess intratester and intertester reliability. RESULTS: There was no significant intratester change in mean. Intratester standard error of measurement was 1.03 mm; 95% confidence intervals were+/-2.02 mm for a single measurement and+/-2.86 mm for a change in measurement. The intratester intra-class correlation coefficient was 0.95. Intertester reliability revealed a significant change in mean between the experienced testers and the novice tester (P<.001). There was no substantial difference for the standard error of measurement of each tester. The mean intertester standard error of measurement was 1.41 mm; 95% confidence intervals were+/-2.77 mm for a single measurement and+/-3.91 mm for a change in measurement. The intertester intraclass correlation coefficient was 0.91. CONCLUSION: Stress radiography was found to be a measurement method with a useful reliability for evaluation of posterior laxity in patients with posterior cruciate ligament lesions. The reproducibility of stress radiography may be influenced by multiple variables, and standardized methods are needed to minimize measurement error.

Arthroscopic evaluation of articular cartilage lesions in posterior-cruciate-ligament-deficient knees.

PURPOSE: The goal of this study was to gain more information on the likelihood of developing cartilage lesions in posterior cruciate ligament (PCL)-deficient knees. TYPE OF STUDY: Retrospective clinical study. METHODS: Standardized arthroscopy records of 181 patients with a nonsurgically treated acute or chronic PCL injury were analyzed with respect to cartilage degeneration. Subgroups with different duration of PCL insufficiency, the influence of isolated PCL or combined PCL/posterolateral instability, and the grade of posterior laxity was analyzed. RESULTS: PCL insufficiency significantly increased the risk of developing medial femoral condyle and patellar cartilage degeneration over time. Of patients whose PCL deficiency was present for more than 5 years, 77.8% showed degenerative cartilage lesions of the medial femoral condyle and 46.7% showed cartilage degeneration of the patella. After 1 year of PCL insufficiency, the number of medial femoral cartilage lesions increased threefold (13.6% v 39.1%). With the presence of combined PCL/posterolateral insufficiency the amount of medial femoral degeneration was significantly increased (36.6% v 60.6%). CONCLUSIONS: We found that PCL insufficiency is not a benign injury with respect to the development of degenerative articular cartilage lesions. The early and continuous increase in cartilage degeneration at the medial femoral condyle and the patella should be considered when discussing operative versus conservative treatment for a PCL-deficient knee. The rapid development of medial arthritis should also be considered during decision making, particularly in patients with combined PCL/posterolateral instability or those who underwent previous partial medial menisectomy.

Fixed posterior subluxation in posterior cruciate ligament-deficient knees: diagnosis and treatment of a new clinical sign.

Among 248 patients seen for posterior cruciate ligament insufficiency, 109 (44%) had fixed posterior subluxation of the tibia, defined as a condition in which posterior sag could not be reduced to a neutral position, as evidenced by posterior tibial displacement of 3 mm or more on anterior stress radiographs at 200 N. The mean fixed posterior displacement was 6.23 mm (range, 3 to 20). The fixed posterior subluxation was divided into three grades: I, 3 to 5 mm (57.8%); II, 6 to 10 mm (33.9%); and III, more than 10 mm (8.3%). Comparison of the 109 study patients with the 139 control patients revealed a history of a failed posterior cruciate ligament operation or of a patellar tendon harvest, male sex, and a long history of posterior cruciate ligament insufficiency as significant risk factors for the development of a fixed posterior subluxation. After patients were treated with a posterior tibial support brace, the fixed posterior subluxation could be reduced to a mean of 2.58 +/- 5.22 mm within an average treatment period of 180 days. Fixed posterior subluxation can be detected in patients with posterior cruciate ligament deficiency by anterior and posterior stress radiographs and should be addressed before posterior cruciate ligament reconstruction to prevent early overloading of the graft.