Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater.

The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota.

INTRODUCTION: Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown. OBJECTIVE: The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS. STUDY DESIGN: Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso. RESULTS: Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (ß-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on ß-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients. CONCLUSION: After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.

[Necrotizing fasciitis of the hand and forearm : Acute surgical treatment and defect reconstruction with MatriDerm® and split-thickness skin graft]. / Nekrotisierende Fasziitis an Hand und Unterarm : Chirurgische Akutversorgung und Defektrekonstruktion mit Spalthaut und MatriDerm®.

This case report describes a 55-year-old male patient with type II necrotizing fasciitis (NF) of the hand and forearm. The rapid progression of the tissue infection could be successfully stopped with radical surgical débridement and antibiotic therapy. For the reconstruction of the extensive loss of soft tissue a combination of split-thickness skin graft (STSG) and the synthetic dermal substitute MatriDerm® was used. In cases of NF, MatriDerm® and STSG provide a rapidly available and simple alternative to other reconstruction techniques.

Letrozole may be a valuable maintenance treatment in high-grade serous ovarian cancer patients.

OBJECTIVES: Endocrine therapy is used as maintenance in estrogen receptor (ER) positive breast cancers and has been proposed in low-grade serous ovarian cancers (LGSOC). Here we examine a rationale for its use as maintenance in high-grade serous ovarian cancers (HGSOC). METHODS: We accessed the TCGA PANCAN dataset to evaluate the expression of ESR1. ESR1 expression data on all cancers (n=8901) and HGSOC (n=527) were followed by investigation of ER expression via immunohistochemistry (IHC) (n=4071). The same was performed in an independent cohort for matched primary and recurrent HGSOC (n=80). Finally, newly diagnosed ER+ HGSOC patients were offered a maintenance therapy with Letrozole. RESULTS: ESR1 was strongly expressed in similar levels in HGSOC as in breast cancer. We found a strong ER expression via IHC in both the primary and matched recurrent HGSOC, particularly in the Platinum-resistant subgroup. The additional use of Letrozole as maintenance treatment was associated with a significantly prolonged recurrence free interval (after 24months 60% when taking Letrozole versus 38.5% in the control group; p=0.035; RFS: IC50 reached by one subject versus 13.2months). This effect was also present in patients treated additionally with Bevacizumab; 20.8% of patients had no recurrence after 12months compared to 87.5% when taking Letrozole in addition to Bevacizumab (p=0.026). CONCLUSIONS: Primary HGSOC have a slightly higher ESR1 than and a similar ER expression breast cancer where aromatase inhibitor maintenance is routine for decades. Here we demonstrate evidence for the usefulness of Letrozole in HGSOC, particularly in patients with chemotherapy resistance or residual disease.

[Pollicization of the Index Finger in Patients with Congenital Thumb Hypoplasia]. / Pollizisation des Zeigefingers bei kongenitaler Daumenhypolasie.

Congenital thumb hypoplasia is a radial deficiency occurring in the form of sole dysplasia or in combination with additional aberrations. Thumb hypoplasia can be categorised into 5 grades ranging from mild deformity to complete absence of the thumb. Thumb hypoplasia leads to a disturbance of grip function depending on its severity. The choice of treatment is based on the degree of thumb hypoplasia. For hypoplasia greater than grade 3B, restoration of the thumb using pollicization of the index finger is the treatment of choice. For this purpose the index finger is transformed into a thumb and is transposed to the position of the thumb with vessels and nerves being retained. The skeleton has to be shortened, rotated and abducted, followed by reconstruction of the muscles in line with the function of the new thumb. This procedure facilitates a restoration with maximal stability, sensitivity and mobility. In cases of isolated thumb hypoplasia, pollicization of the index finger yields good results persisting into adulthood. If associated aberrations are present, the outcome is less predictable because of the preexistent stiffness of the index finger. Nevertheless, associated aberrations do not represent a contraindication for index finger pollicization.

Limited hepatitis B immunoglobulin with potent nucleos(t)ide analogue is a cost-effective prophylaxis against hepatitis B virus after liver transplantation.

BACKGROUND: Prophylaxis against hepatitis B virus (HBV) recurrence after orthotopic liver transplantation (OLT) includes lifelong hepatitis B immunoglobulin (HBIG) and oral antiviral agent(s). In the presence of high-genetic-barrier nucleos(t)ide analogues, the need for lifelong HBIG is questioned. We evaluated the safety and cost-effectiveness of a limited HBIG course. METHODS: OLT from 2006 to 2013 were reviewed. Patients with pre-OLT hepatitis B virus surface antigen who received HBV prophylaxis with 2 HBIG doses (anhepatic and first post-operative day; 10,000 units/dose) and potent nucleos(t)ide analogues were included. The primary end point was HBV recurrence (HBV-DNA detection). RESULTS: Thirteen patients (primary transplants) were included, median Model for End-Stage Liver Disease score was 18, and there was no fulminant failure; HBV-DNA was detected in 4 patients at OLT. After OLT, 10 patients received entecavir and/or tenofovir. Median follow-up was 23 months. One recurrence occurred (7.7%) at month 13 (HBV-DNA: 14 IU/mL); the graft maintained excellent function. This minimal viremic expression is related to hepatocellular carcinoma recurrence with neoplastic replication carrying integrated HBV-DNA; thus, there is no defined HBV viral recurrence. No graft loss or patient death was related to HBV recurrence. The 1-year patient and graft survival rate was 84.6%. Cost-savings in the first year was $178,100 per patient when compared with Food and Drug Administration-approved HBIG dosing. CONCLUSIONS: In the era of potent oral nucleos(t)ide analogues, a limited HBIG course appears to be cost-effective in preventing HBV recurrence.

Perforated sigmoid diverticulitis in the presence of toxic epidermal necrolysis.

Even though the incidence of toxic epidermal necrolysis (TEN) is low, it is also associated with a high mortality rate. The condition predominantly affects the skin, but may also affect the gastrointestinal tract, dramatically increasing mortality. We present a case of perforated sigmoid diverticulitis in the presence of TEN. The patient was taking medication, known to be a risk factor, and presented an affected total body surface area and temporal development similar to previously reported cases of TEN. Characteristic abdominal symptoms, however, were missing. Gastrointestinal involvement in TEN appears to be a poor prognostic factor; medical staff must therefore be alert to patients with TEN who complain of abdominal discomfort. The exact pathogenesis, however, remains unclear.

The epidemiology of knee injuries in children and adolescents.

BACKGROUND: Injuries in childhood and adolescence are frequent and the knee is one of the most common sites of injuries. This study aimed to analyze the epidemiology, gender distribution, age, and circumstances of knee injuries in childhood at a Level I Trauma Center in Austria. METHODS: All pediatric and adolescent trauma patients who presented in a 2-year period were recorded. Children managed with knee injuries were selected prospectively. Patients were divided into five age groups: infants (younger than 1 year); pre-school aged children (1-6 years); pre-pubertal school-aged children (7-10 years); early adolescent patients (11-14 years); and late adolescent patients (15-18 years). Five diagnosis-related groups were formed: extraarticular soft tissue injuries, intraarticular soft tissue injuries, patella disorders, fractures, and overload injuries. RESULTS: The study included 23,832 patients up to the age of 18 years, who presented with 1,199 knee injuries. There was a male predominance (m:f = 58,6%:41.4%). Boys had a lower mean age at presentation (11.9 years) as girls (12.3 years). The most common accident sites were outdoors (34.8%) and sports facilities (32.8%). Leading injury mechanisms were falls on level surfaces (58.1%) and traffic accidents (13.4%). The number of knee injuries and its severity increased with age. Knee injuries did not occur in infants. In general, extraarticular soft-tissue injuries were most common and fractures were rare. CONCLUSION: Knee injuries in children and adolescents are rare and extraarticular soft-tissue injury is the most frequent type of knee trauma. The number of knee injuries and its severity increases with age with a male predominance. Sports facilities and traffic injuries are important scenes of knee trauma. Mechanisms and patterns evaluated in this study can serve as the basis for knee-injury prevention efforts in children and adolescents and may be used for necessary precautions. LEVEL OF EVIDENCE: IV.

[Traumatic posterior dislocation of the sternoclavicular joint. A case report of joint stabilization with gracilis tendon graft]. / Die traumatische posteriore Luxation im Sternoklavikulargelenk. Fallpräsentation einer Stabilisierung mit Grazilissehnenplastik.

Dislocation of the sternoclavicular joint is an uncommon injury. Especially posterior dislocations with potentially life-threatening complications present a challenging situation for the treating surgeon regarding diagnosis and therapy. Reduction and fixation of the joint is the treatment of choice. We present the case of such an injury in an adolescent judoka who was treated by open reduction and reconstructive surgery using the gracilis tendon graft technique.

Intramedullary nailing for the treatment of dislocated pediatric radial neck fractures.

INTRODUCTION: Pediatric radial neck fractures represent 5-10% of all elbow fractures. Open reduction allows anatomic fracture fixation but compromises the vulnerable blood supply of the radial head. Intramedullary nailing combines the advantages of closed reduction and stable internal fracture fixation. MATERIAL AND METHODS: During a 6-year-period the medical records of all children sustaining a radial neck fracture treated operatively at our institution were analyzed retrospectively. RESULTS: Forty-two patients with dislocated fractures of the radial neck were treated with intramedullary nailing. The average age of the patients was 8 years. Thirty-eight patients (90%) could be treated with closed fracture reduction and retrograde nailing. Open fracture reduction was required in 4 (10%) patients, and in 2 patients necrosis of the radial head occurred. Loss of reduction was seen in 7 (17%) patients. Excellent results were found in 38 patients, good results in 2 patients, and poor results in another 2. CONCLUSION: The retrograde nailing technique for the treatment of dislocated fractures of the radial neck in pediatric patients is a simple, short and safe procedure.

[Torsion of a pedunculated subserous myoma - a rare differential diagnosis of the acute abdomen]. / Torsion eines gestielten subserösen Myoms - eine seltene Differentialdiagnose des akuten Abdomens.

We report about a rare case of acute abdomen in a 43 years old female patient who noticed a sudden onset of severe lower abdominal pain, increasing in strength within a few hours. The transabdominal and transvaginal ultrasound showed an enlarged leiomyomatous uterus with a questionable torsion of a pedunculated subserous leiomyoma. The following magnetic resonance imaging confirms this diagnosis. During the laparoscopy a myomectomy has been performed.

Prognostic and predictive value of TOPK stratified by KRAS and BRAF gene alterations in sporadic, hereditary and metastatic colorectal cancer patients.

BACKGROUND: Our aim was to investigate the prognostic and predictive value of the oncogenic MAPKK-like protein T-cell-originated protein kinase (TOPK) stratified by KRAS and BRAF mutations in patients with sporadic, hereditary and metastatic colorectal cancer (CRC) treated with anti-EGFR therapy. METHODS: Immunohistochemistry (IHC) for TOPK was performed on four study groups. Group 1 included two subgroups of 543 and 501 sporadic CRC patients used to test the reliability of TOPK expression by IHC. In Group 2, representing an additional 222 sporadic CRCs, the prognostic effect of TOPK stratified by KRAS and BRAF was assessed. The prognostic effect of TOPK was further analysed in Group 3, representing 71 hereditary Lynch syndrome-associated CRC patients. In Group 4, the predictive and prognostic value of TOPK was analysed on 45 metastatic patients treated with cetuximab or panitumumab stratified by KRAS and BRAF gene status. RESULTS: In both sporadic CRC subgroups (Group 1), associations of diffuse TOPK expression with clinicopathological features were reproducible. Molecular analysis of sporadic CRCs in Group 2 showed that diffuse TOPK expression was associated with KRAS and BRAF mutations (p<0.001) and with poor outcome in patients with either mutation in univariate and multivariate analysis (P=0.017). In hereditary patients (Group 3), diffuse TOPK was linked to advanced pT stage. In metastatic patients treated with anti-EGFR therapy (Group 4), diffuse TOPK expression was linked to dismal outcome despite objective response to treatment (P=0.01). CONCLUSIONS: TOPK expression is an unfavourable prognostic indicator in sporadic patients with KRAS or BRAF mutations and also in patients with metastatic disease experiencing a response to anti-EGFR therapies. The inhibition of TOPK, which could benefit 30-40% of CRC patients, may represent a new avenue of investigation for targeted therapy.

Metastatic involvement of the urinary tract in patients with advanced ovarian carcinoma: lessons from the autopsy for an interdisciplinary treatment approach.

PURPOSE OF INVESTIGATION: Frequency and extent of metastases in urologic organs found at autopsy of ovarian carcinoma patients were evaluated. METHODS: Autopsy reports from 170 patients who died of advanced ovarian carcinoma between 1975 and 2005 were studied. The distribution of abdominal metastatic sites with particular attention to the involvement of the urologic organs, and hydronephrosis was analyzed. RESULTS: The distribution of metastatic sites was as follows: kidney (n = 6, 3.5%), urinary bladder (n = 38, 22.4%), and ureter (n = 20, 11.8%). In 36 patients, hydronephrosis was observed (21.2%); of these patients, 20 (55.6%) also had ureteral involvement. All patients with ureteral involvement had hydronephrosis. CONCLUSION: Hydronephrosis in late stages of ovarian carcinoma, usually attributed to extrinsic compression of the ureter by an abdominal tumor, may also be explained by ureteral metastases. This fact must be considered in the clinical management of these patients, particularly in the restoration of luminal patency through an endoscopically placed internal ureteral stent.

[Stereotactic Mammotome breast biopsy: routine clinical experience and correlation with BI-RADS--classification and histopathology]. / Die stereotaktische Mammotome-Brustbiopsie: Erfahrungen im klinischen Alltag und Korrelation der BI-RADS--Klassifikation mit der Histopathologie.

BACKGROUND: Stereotactic breast biopsy using the Mammotome system allows minimal invasive tissue sampling of suspicious lesions of the breast cancer, e.g. clustered microcalcifications BI-RADS type 3 and 4, and has widely replaced open surgical biopsies. The aim of this retrospective study was to review the results of these biopsies in regard of technical feasibility and complications as well as to correlate initial BI-RADS assessment with histopathology. METHODS: One hundred thirty-five vacuum-assisted breast biopsies in 124 patients were evaluated. Before biopsy, the mammograms were classified according to the Breast Imaging Reporting and Data System (BI-RADS). All mammograms were reviewed with knowledge of the final histologic diagnosis. Patients with benign diagnoses underwent mammographic follow-up. Excisional biopsy was recommended for diagnoses of in-situ or invasive carcinoma. RESULTS: No serious complications of the biopsies were observed. Histopathology revealed 105 (78%) benign lesions. Benign lesions were classified as BI-RADS 3 in 49 (36%) and as suspicious (BI-RADS 4) in 56 (41%). Thirty lesions (22%) were malignant, of which 26 (87%) were classified BI-RADS 4 or 5. The frequency of malignancy in BI-RADS 4 and 5 was 19 of 75 (25%) and 7 of 7 (100%), respectively. Of the 53 BI-RADS 3 lesions, 4 (8%) were malignant. CONCLUSIONS: Mammotome biopsy was shown to be a safe and well-tolerated technique for the work-up of mammographic lesions. The frequency of malignant histopathologic findings in BI-RADS 3 lesions was higher than expected, reflecting the difficulties in the mammographic differentiation of benign and malignant clustered microcalcifications.

[Meningothelial meningioma in a mature cystic teratoma of the ovary]. / Meningotheliomatöses Meningeom in einem reifen zystischen Teratom des Ovars.

Mature teratomas belong to the group of germ cell tumors of the ovary. They account for 27-44% of all ovarian neoplasms and up to 58% of all benign tumors of the ovary. In mature as well as in immature teratomas, secondary tumors originating from the three embryonic tissue components may be found. These tumors can show benign or malignant behavior. We report the case of a meningothelial meningioma, found within a mature teratoma of a 32 year old female. The characteristic histomorphology and immunohistochemical expression for epithelial membrane antigen (EMA) and desmoplakin are diagnostic.

[Ectopic prostatic tissue in the uterine cervix]. / Ektopes Prostatagewebe in der Cervix uteri.

Ectopic prostate tissue is a rare occurrence in the lower female genital tract. Possible theories of histogenesis include a developmental anomaly, metaplasia of preexisting endocervical glands, and derivation from mesonephric remnants. We report an example of prostatic tissue involving the uterine cervix of an 82-year-old woman as an incidental finding in a hysterectomy specimen. This unusual lesion should be differentiated from atypical glandular lesions of the cervix. Immunohistochemical studies confirm the histological suspicion of ectopic prostatic tissue.

Bilateral periprosthetic stress fractures in a juvenile chronic arthritis patient secondary to bilateral genu valgum.

Lateral insufficiency fractures following total hip replacement have been reported with the femoral stems positioned in varus, together with osteopenia of the lateral femoral cortex. Any abnormal alignment of the lower limbs, such as genu valgum, will alter the load distribution across the femoral cortices, and repetitive loading during walking will predispose the bones to stress fractures at any stress riser point, such as the tip of a femoral component. Bilateral femoral stress fractures post total hip replacements have not been previously described. We present a 55-year-old woman, diagnosed with juvenile idiopathic arthritis, who had undergone bilateral total hip replacements and bilateral knee replacements. The knees 15 years postoperatively were in valgus and the left knee was extremely stiff, flexing to just 5. The patient presented with bilateral thigh pain, with plain radiographs confirming bilateral periprosthetic fractures of the femur at the tip of well-fixed femoral components. There was no history of injury and her hips were functioning well up to this time. The patient required revision of both hips to long-stem uncemented components, bypassing the fractures, and revision of both knees to stemmed semi-constrained implants, thereby correcting the alignment of both lower limbs. Both fractures healed and the patient is currently pain-free and mobile with walking aids. Surgeons must remain aware that when implants are in situ, abnormal alignments will lead to abnormal forces, and stress fractures are likely to occur at any stress riser around the implant. Avoiding malalignment will avoid this complication.

Femoral stem tip orientation and surgical approach in total hip arthroplasty.

INTRODUCTION: A posterior entry point, a neutral tip position and neutral stem alignment are recommended to avoid a thin cement mantle and ensure an optimal outcome in total hip arthroplasty (THA). Our aim was to highlight any influence of surgical approach in obtaining an optimal stem orientation. METHODS: We examined the post-operative, digitised radiographs of 100 (50 each group) polished, tapered Exeter THA, inserted via the antero-lateral or posterior approaches. Stem tip position was assessed in both coronal and sagittal planes and stem alignment was assessed in the coronal plane. RESULTS: There was a significant difference between the two approaches in the sagittal stem tip position only (p=0.01). DISCUSSION: Our results illustrate that a neutral stem tip position in THA is significantly more difficult to obtain with an antero-lateral approach, when compared to the posterior approach. A posterior approach to the hip avoids the cuff of glutei that can lever the proximal stem anteriorly causing an anterior entry point and a posterior stem tip position. We also illustrate how the anatomy of the proximal femur in the sagittal plane makes a neutral stem alignment difficult to achieve with either approach.