Amplification Rate Research Articles

Experimental research on self-amplifying density waves in horizontal pipelines of two phase granular slurries: Measurements on the effect of particle diameter and concentration

Self-amplifying density waves in hydraulic transport pipelines is a scarcely researched topic. Density waves are in essence the result of a spatial redistributing effect and clustering of solids in hydraulic transport pipelines. Self-amplifying density waves are very undesirable for practical applications, as these waves increasing the risk of pipeline blockages. The two available experimental studies (Talmon et al., 2007; Matoušek and Krupička, 2013) report conflicting properties of the density waves, such as wave length and wave celerity. This new experimental research aims to shed light on the reported differences, by broadly varying particle size and concentration in a new dedicated experiment. The main highlight of this research is that two separate mechanisms were identified that can cause density waves, and Talmon et al. (2007) and Matoušek and Krupička (2013) in hindsight were studying the two different mechanism respectively. Both wave type mechanisms come into effect at mixture velocities close to the deposit limit velocity, and require a stationary bed layer to initiate. The first mechanism is caused by an imbalance of erosion and sedimentation of the bed layer, which is predominant for fine sand particles (∼242μm and ∼308μm in this research). The second mechanism occurs when the bed layer starts sliding, instead of being eroded, and is specific for larger sand sizes (∼617μm and ∼1.08mm in this research). These two mechanisms are clearly distinguishable, having different wave lengths, celerity, amplitudes and amplification rates. The results also show a clear relationship between the mean concentration of a density wave, the wave amplitude and wave celerity specific for each of the two mechanisms.

A novel cellular structure with center-symmetric cell walls for morphing applications

Cellular structures are potential candidates for the supporting framework of flexible morphing skins. Unlike traditional zero Poisson’s ratio (ZPR) cellular structures with axisymmetric cell walls, this paper proposes a novel cellular structure with center-symmetric cell walls. The in-plane mechanical properties of this novel structure are explored through theoretical analysis and substantiated by both finite element simulations and experimental tests. Compared to the classic accordion honeycomb structure, the elastic modulus in the x-direction of the novel structure is reduced by an average of 58%, the strain amplification rate is increased by 122%, and the in-plane stiffness anisotropy is improved by 200%. These findings suggest that the proposed structure offers far superior stiffness anisotropy and large deformation potential, making it more suitable for morphing applications than the traditional ZPR cellular structures.

Robotic Manipulation of Cumulus–Oocyte Complexes for Cumulus Cell Removal

The removal of cumulus cells from cumulus–oocyte complexes is a critical step in clinical in vitro fertilization. Since the oocyte is partially occluded by the surrounding cumulus cells and individual cumulus cells are small in size, it is difficult for embryologists to assess the oocyte's maturity before cumulus cell removal and to completely remove all the cumulus cells manually . Furthermore, it is easy for the oocyte to become lost inside the micropipette during aspiration due to the inaccuracy of manual control. To deal with these difficulties, a robotic system was developed to completely remove cumulus cells from mature oocytes. In this study, an EPSANet50 network was developed to accurately assess the maturity of oocytes, avoiding the removal of cumulus cells around the immature oocyte. An adaptive controller was designed to accurately position oocytes at the target position, reducing the loss of oocytes inside the micropipette. An improved Yolov5s network was proposed to quantify the number and size of cumulus cells and assess the completeness of cumulus cell removal. The experimental results on mouse cumulus–oocyte complexes showed that the robotic system had a higher success rate (98.0 ± 1.8% vs. 85.3 ± 2.4%) and lower discard rate (4.1 ± 2.7% vs. 19.6 ± 3.5%) than the manual operation. Moreover, a higher amplification rate and lower non-specific rate were also achieved by the robotic system in the subsequent genetic testing procedure, indicating reduced genetic contamination from the cumulus cells.

Ultrafast DNA detection based on turn-back loop primer-accelerated LAMP (TLAMP)

Rapid DNA detection is a long-pursuing goal in molecular detection, especially in combating infectious diseases. Loop-mediated isothermal amplification (LAMP) is a robust and prevailing DNA detection method in pathogen detection, which has been drawing broad interest in improving its performance. Herein, we reported a new strategy and developed a new LAMP variant named TLAMP with a superior amplification rate. In this strategy, the turn-back loop primers (TLPs) were devised by ingeniously extending the 5’ end of the original loop primer, which conferred the new role of being the inner primer for TLPs while retaining its original function as the loop primer. In theory, based on the bifunctional TLPs, a total of eight basic dumbbell-like structures and four cyclic amplification pathways were produced to significantly enhance the amplification efficiency of TLAMP. With the enhancing effect of TLPs, TLAMP exhibited a significantly reduced amplification-to-result time compared to the conventional six-primer LAMP (typically 1 h), enabling rapid DNA detection within 20 min. Furthermore, TLAMP proved to be about 10 min faster than the fast LAMP variants reported so far, while still presenting comparable sensitivity and higher repeatability. Finally, TLAMP successfully achieved an ultrafast diagnosis of Monkeypox virus (MPXV), capable of detecting as few as 10 copies (0.67copies/μL) of pseudovirus within 20 min using real-time fluorescence assay or within 30 min using a colorimetric assay, suggesting that the proposed TLAMP offers a sensitive, specific, reliable, and, most importantly, ultrafast DNA detection method when facing the challenges posed by infectious diseases.

TP53 and EGFR amplification are negative predictors of overall survival in patients diagnosed with non-small cell lung cancer with brain metastases

BackgroundThe discovery of driver genes such as EGFR, KRAS, and ALK, has dramatically shifted treatment patterns in patients harboring these oncogenes. However, dissemination into the central nervous system (CNS) is a severe complication. In addition, the particular anatomical structure of the CNS has made it difficult to obtain tissue specimens from brain metastases (BM) to generate a gene map, as such, potential predictive markers for survival in patients with non-small cell lung cancer (NSCLC) and BM (NSCLC-BM) remain unclear. MethodsData from 28 patients diagnosed with NSCLC-BM between June 2019 and May 2021 at Guangdong Sanjiu Brain Hospital (Guangzhou, China), were reviewed. Targeted next-generation sequencing (NGS) of a 168 cancer-related gene panel was available for surgically resected brain tissues from all patients. In addition, molecular characteristics and overall survival (OS) were analyzed to determine potential predictive markers. ResultsAmong patients with NSCLC-BM, NGS revealed that TP53 was the most frequent mutation (61 %), with a detection rate of 39 %, closely by EGFR amplification. Additionally, CDKN2A, MYC, LRP1B, and RNF43 were frequently observed (18 %). The median OS was significantly shorter in the TP53 mutation group than in the wildtype group (14 versus undefined months, p = 0.014). Similar results were also found in the genetic alteration of EGFR amplification, suggesting that EGFR amplification was associated with worse OS (14 vs. 24 months, p = 0.039). Interestingly, NGS revealed that gene alternations such as TP53, EGFR amplification, and CDKN2A, tended to coexist and such a co-alteration panel indicated worse clinical outcomes (median OS, 5 months). In addition, the detection rate of negative survival genes, including TP53 or EGFR amplification, was much higher in tumor tissues than in plasma samples, indicating the limited predictive value of matched PLA samples. ConclusionsGene signatures, such as TP53 or EGFR amplification, were associated with worse survival in patients diagnosed with NSCLC-BM. These valuable findings may shed light on new strategies for the prognostic assessment of specific patient groups.

Successful development of molecular diagnostic technology combining mini-barcoding and high-resolution melting for traditional Chinese medicine agarwood species based on single-nucleotide polymorphism in the chloroplast genome.

Agarwood is a valuable traditional medicine and fragrance. The production process is a typical injury-induced defense response. Currently, there are approximately 22 known species in the genus Aquilaria Lam., all of which can produce agarwood, whereas there are only two legal species of traditional Chinese medicinal agarwood, Aquilaria sinensis (Lour.) Spreng. and Aquilaria agallocha (Lour.) Roxb. The Taiwan herbal Pharmacopoeia of China stipulates that the medicinal agarwood species are A. sinensis and its relatives in the same genus. Moreover, there are five species of agarwood available for clinical medicinal use in Japan, including A. agallocha and A. sinensis, which are often confused with each other or used in a mixed way in the trade process. Therefore, accurate identification of traditional Chinese medicinal agarwood species is important to ensure the authenticity of traditional medicines and to guide the safety of clinical medication. In this study, 59 specific single-nucleotide polymorphism loci were screened and obtained from the chloroplast genomes of 12 species of the genus Aquilaria Lam. We established an identification method for traditional Chinese medicinal agarwood using mini-barcoding combined with high-resolution melting (HRM) and designed and validated 10 pairs of primers from the psbM-trnD, psbA, rps16, petN, ndhE-psaC, rps4, atpE, ycf1, rps15-trnN, and matK regions. The amplification products were all less than 200 bp, with a high success rate of amplification. The method was applied to successfully identify traditional Chinese medicinal agarwood species from commercial agarwood samples. Overall, the sensitivity of this method was sufficient to detect 1% of adulterants in medicinal agarwood products, proving that mini-barcoding HRM is a powerful and flexible tool. This method can be used as a fast and effective high-throughput method for authenticity testing of traditional Chinese medicinal agarwood and its raw materials containing agarwood-containing proprietary Chinese medicines and is recommended for industrial applications.

NGS and FISH for MET amplification detection in EGFR TKI resistant non-small cell lung cancer (NSCLC) patients: A prospective, multicenter study in China

ObjectivesComprehensive data using Next-Generation Sequence (NGS) and fluorescence in situ hybridization (FISH) for detecting MET amplification is limited in Chinese patients, we evaluating NGS performance both in tissue and plasma samples using FISH as reference. We also sought to find optimal thresholds value for NGS in detecting MET amplification via bioinformatics methods. MethodPatients progressed after 1st-, 2nd-, or 3rd-generation (G) EGFR-TKIs were enrolled. Tissue biopsy samples were performed for MET amplification detection via both NGS and FISH. Paired plasma samples were collected for MET amplification detection by NGS. The sensitivity, specificity and agreement were analyzed between NGS and FISH. Results116 eligible patients were analyzed. 44 patients were male. 82 patients were after 3rd generation EGFR-TKI. MET amplification was detected in 43 (37.1 %) patients by FISH, including 19 (16.4 %) polysomy and 24 (20.7 %) focal amplification. The positive rate of MET amplification in post 3rd generation EGFR-TKI and post 1st/2ndgeneration EGFR-TKI resistant patients was 42.7 % (35/82), and 23.5 % (8/34).The sensitivity, specificity and agreement of detecting MET amplification by NGS in tissue were 39.5 % (17/43), 98.6 % (72/73) and 76.7 % (89/116), respectively, 66.7 % (16/24), 98.6 % (72/73) and 90.7 % (88/97) for focal MET amplification in tissue and 29.2 % (7/24), 94.5 % (69/73), 78.4 % (76/97) for focal amplification in plasma. Results were shown in the table below. ConclusionNGS is an alternative method for MET focal amplification detection in tissue. While the sensitivity of NGS testing in plasma needs further improvement to maximize identification of patients with potential benefit from dual-targeted therapy.

Fabrication of Cost-Effective Microchip-Based Device Using Sandblasting Technique for Real-Time Multiplex PCR Detection.

The combination of multiplex polymerase chain reaction (mPCR) and microfluidic technologies demonstrates great significance in biomedical applications. However, current microfluidics-based molecular diagnostics face challenges in multi-target detection due to their limited fluorescence channels, complicated fabrication process, and high cost. In this research, we proposed a cost-effective sandblasting method for manufacturing silicon microchips and a chip-based microdevice for field mPCR detection. The atomic force microscopy (AFM) images showed a rough surface of the sandblasted microchips, leading to poor biocompatibility. To relieve the inhibitory effect, we dip-coated a layer of bovine serum albumin (BSA) on the irregular substrate. The optimized coating condition was determined by scanning electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDS) (65 °C for 60 min). After sufficient coating, we performed on-chip PCR tests with 500 copies/mL Coronavirus Disease 2019 (COVID-19) standard sample within 20 min, and the sandblasted microchip displayed a higher amplification rate compared to dry etching chips. Finally, we achieved a 50 min mPCR for screening five resistance genes of the endophthalmitis pathogens on our microdevices, with strong specificity and reliability. Thus, this sandblasted microchip-based platform not only provides a rapid, accessible, and effective solution for multiplex molecular detection but also enables large-scale microfabrication in a low-cost and convenient way.

Evaluation of ITS1 rDNA primers for the detection and identification of African trypanosomes in mammalian hosts and tsetse flies.

Although several primers targeted to the internal transcribed-spacer 1 (ITS1) of the ribosomal DNA (rDNA) have been designed to improve the detection of African trypanosomes, no study tried to compare their agreement level and ability to amplify different trypanosome species in tsetse flies and mammals in various epidemiological settings. This study was designed to fill this gap, by targeting tsetse-infested areas of Cameroon. For this, archived DNA samples reporting at-least one trypanosome species with species-specific PCR primers were reviewed. Ten sets of primers targeting different ITS1 rDNA sequences of trypanosomes were selected for assessment using single-round and nested-PCR method. Amplification rates (sensitivity) and agreement level of different ITS1 assays were compared using Cohen's-Kappa and McNemar's x2 statistic. Little agreement level (k = 0.05–0.52) were observed between different ITS1-primers PCRs detection of African trypanosome species despite significant (X2=54.3, p = 0.0001) high amplification rate 91.6 % (339/370). This sensitivity varied from quite low for T. simiae (11.9 %) and T. vivax (27.3 %) to fairly good for T. congolence (51.9 %), Trypanozoon (32.4 %) and T. theileri (40.3 %). Primers set targeting ITS1-A sequence of trypanosome species recorded the highest sensitivity (50.5 %) with fairly good agreement compared to 39.2 % for ITS1-C (k = 0.52), 32.4 % for ITS1-R (k = 0.47), 29.7 % for ITS1-N (k = 0.48) and 23.0 % for ITS1-KIN (k = 0.43) respectively. This study revealed a diversity in the sensitivity of different trypanosome species with different sets of ITS-primers enhancing the need to use the same sets of primers in different bio-ecological settings. The use of nested-PCR instead of single-round PCR enabled improvement of trypanosome infections detection in both tsetse and mammals. Among the sets of ITS1-primers tested, those designed by to amplify ITS1-A can be considered as the most appropriate for the detection of trypanosome infections in mammals and tsetse flies.

Effect of Phlebotomus papatasi on the fitness, infectivity and antimony-resistance phenotype of antimony-resistant Leishmania major Mon-25

Leishmania major is responsible for zoonotic cutaneous leishmaniasis. Therapy is mainly based on the use of antimony-based drugs; however, treatment failures and illness relapses were reported. Although studies were developed to understand mechanisms of drug resistance, the interactions of resistant parasites with their reservoir hosts and vectors remain poorly understood. Here we compared the development of two L. major MON-25 trivalent antimony-resistant lines, selected by a stepwise in vitro Sb(III)-drug pressure, to their wild-type parent line in the natural vector Phlebotomus papatasi. The intensity of infection, parasite location and morphological forms were compared by microscopy. Parasite growth curves and IC50 values have been determined before and after the passage in Ph. papatasi. qPCR was used to assess the amplification rates of some antimony-resistance gene markers. In the digestive tract of sand flies, Sb(III)-resistant lines developed similar infection rates as the wild-type lines during the early-stage infections, but significant differences were observed during the late-stage of the infections. Thus, on day 7 p. i., resistant lines showed lower representation of heavy infections with colonization of the stomodeal valve and lower percentage of metacyclic promastigote forms in comparison to wild-type strains. Observed differences between both resistant lines suggest that the level of Sb(III)-resistance negatively correlates with the quality of the development in the vector. Nevertheless, both resistant lines developed mature infections with the presence of infective metacyclic forms in almost half of infected sandflies. The passage of parasites through the sand fly guts does not significantly influence their capacity to multiply in vitro. The IC50 values and molecular analysis of antimony-resistance genes showed that the resistant phenotype of Sb(III)-resistant parasites is maintained after passage through the sand fly. Sb(III)-resistant lines of L. major MON-25 were able to produce mature infections in Ph. papatasi suggesting a possible circulation in the field using this vector.

Significance of concurrent evaluation of HER2 gene amplification and p53 and Ki67 expression in gastric cancer tissues.

The primary objective of this study is to explore the significance of concurrent evaluation of HER2 gene amplification and p53 and Ki67 expression in gastric cancer tissues. Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) methodologies were used to detect HER2 gene amplification, as well as the expression levels of HER2, p53, and Ki67 proteins, across a group of 78 gastric cancer cases. The expression rate of the HER2 protein was determined to be 43.6% (34/78), with 17.9% (14/78) categorized as HER2 protein 3 + , 14.1% (11/78) as HER2 protein 2 + , and 11.5% (9/78) as HER2 protein 1 + . Using FISH technology, the HER2 gene amplification rate was identified as 19.2% (15/78), including 3 cases of HER2 gene cluster amplification, 5 cases of large granular amplification, 4 cases of punctate amplification, and 3 cases of high polysomy. The positive rate of p53 in gastric cancer cells was 52.6% (41/78), with 62.8% (49/78) of patients exhibiting a ki67 proliferation index ≤ 30, and 37.2% (29/78) accounting for a ki67 proliferation index > 30. The expression rates of the HER2 gene, p53, and ki67 in gastric cancer tissues were significantly associated with both gastric cancer staging and lymph node metastasis (P < 0.05). The HER2 gene amplification rate and gene copy number exhibit a positive correlation with the expression rates of p53 and ki67. Combining these assessments can provide crucial insights into the assessment of metastatic potential, disease progression, and prognosis of gastric tumor cells. This holds paramount importance in steering the formulation of individualized treatment strategies.

Uncovering the Past: DNA Analysis of Skeletal Remains from the Medieval Bosnian City of Bobovac

Numerous archaeological sites in Bosnia and Herzegovina represent a historical heritage and testify to the rich cultural, social, and political life of medieval Bosnia. Bobovac, the capital of the Bosnian Kingdom after King Tvrtko I's coronation in 1377, featured a royal complex with a palace, church, and fortification. Recent molecular-genetic research on skeletal remains from Bobovac aims to uncover medieval ancestors' customs and genetic origins. Fifteen well-preserved teeth samples from Bobovac were processed. STR amplification employed PowerPlex® Fusion and Investigator® 24plex QS Kits, with Y-STR profiles generated using the PowerPlex® Y23 System. Fourteen partial autosomal STR profiles were obtained, enabling sex determination and kinship analysis. STR amplification success varied due to ancient DNA degradation, with larger loci showing lower amplification rates. Kinship analysis confirmed appropriate marker selection, demonstrating high reliability for determining close relationships. Integrating aDNA analysis with archaeological research enhances our understanding of historical populations, connecting archaeology and forensic genetics to contribute to the broader narrative of human history.

Non-Oberbeck–Boussinesq effects on the linear stability of a vertical natural convection boundary layer

The non-Oberbeck–Boussinesq effects on the stability of a vertical natural convection boundary layer are investigated using the linearised disturbance equations for air flows up to a temperature difference of $\Delta T=100\,{\rm K}$ . Based on the linear stability results, the neutral curve is shown to be sensitive to the choice of reference temperature. When evaluated using the film temperature $T_f$ , a lower film Grashof number is required to trigger the linear instability for larger $\Delta T$ . The relative contributions of shear and buoyant production to the perturbation kinetic energy budget reveals that the marginally unstable modes are amplified based on different mechanisms: for lower wavenumbers at relatively small Grashof number, the instability is driven by buoyancy; whereas for higher wavenumbers and larger Grashof number, the flow becomes unstable due to a shear instability. The use of reference temperature is found to scale the shear- and buoyant-driven instabilities differently so that no single reference temperature definition would collapse the neutral curves. The linear stability result further demonstrates that at a given Grashof number a higher temperature difference would give a larger amplification rate of the perturbation, which then leads to an earlier onset of the nonlinearities when evaluated at $T_f$ . Finally, by comparing the amplification rates obtained from direct numerical simulation and the linear stability results, the extent of the linear regime is determined for $\Delta T = 100\,{\rm K}$ .

Her-2/neu gene amplification and its correlation with other prognostic factors in Iranian breast cancer patients.

Breast cancer is one of the most common diseases in females, arising from overexpression of a variety of oncogenes like HER2/neu. The amplification rate of this gene is variable in different breast cancer patients. In this study, the amplification of the HER2/neu oncogene was distinguished in breast cancer patients and its correlation with prognostic factors. Also, the simultaneous effect of prognostic factors on the occurrence of a specific prognostic factor was investigated. The multiplex PCR technique was used to assay the amplification of the HER2/neu oncogene in breast cancer patients. After extracting DNA from 100 tumor tissue and 8 normal breast tissue samples, the amplification of the HER2/neu gene was distinguished by the co-amplification of a single-copy reference gene, γ-IFN, and the target gene HER2/neu in the PCR reaction and using the Gel analyzer software. SPSS 23 and STATA 9.1 software were used for statistical analysis. The HER2/neu gene was amplification in 30% of the tumor samples. The statistical analysis showed a statistically significant relationship between HER2/neu gene amplification and progesterone receptors. Amplification of the HER2/neu gene significantly increases the chance of lymph node involvement. Also, the amplification of this gene in tumors with histological grade II tissue is more than grade I. The amplification of the HER2/neu gene can be used as an independent prognostic factor in predicting lymph node involvement and histological grade in breast cancer patients.

Comparing the advantages, disadvantages and diagnostic power of different non-invasive pre-implantation genetic testing: A literature review.

To improve embryo transfer success and increase the chances of live birth in assisted reproductive methods, there is a growing demand for the use of pre-implantation genetic testing (PGT). However, the invasive approaches used in PGT have led to in vitrofertilization failure and abortions, increasing anxiety levels for parents. To address this, non-invasive PGT methods have been introduced, such as the detection of DNA in blastocoel fluid of blastocysts and spent culture media (SCM). These methods have proven to be minimally invasive and effective in detecting aneuploidy in the chromosomes of human embryos. This review aims to explore the different approaches to pre-implantation diagnosis, including invasive and non-invasive methods, with a particular focus on non-invasive PGT (niPGT). The search strategy involved gathering data from scientific databases such as PubMed, Google Scholar, and Science Direct using relevant keywords. The search was conducted until January 2023. In total, 22 studies have successfully reported the detection and amplification of cell-free DNA in the embryonic SCM. It is important to note that niPGT has some limitations, which include differences in indicators such as cell-free DNA amplification rate, concordance, level of maternal DNA contamination, sensitivity, and specificity between SCM samples and biopsied cells. Therefore, more extensive and detailed research is needed to fully understand niPGT's potential for clinical applications.

EGFR, HER2, and MET gene amplification and protein expression profiles in biliary tract cancer and their prognostic significance.

There are limited conventional chemotherapy options for biliary tract cancers (BTCs), a heterogenous group of lethal, rare malignancies. The receptor tyrosine kinase (RTK) is closely associated with the progression of human malignancies through the regulation of cell cycle. Overexpression or amplification of RTKs has been investigated as a potential biomarker and therapeutic target in BTC; herein, we investigate the value of such interventions. Overexpression of RTK proteins was examined by immunohistochemistry in 193 BTC samples, of which 137 were gallbladder carcinoma, 29 were perihilar cholangiocarcinoma, and 27 were intrahepatic cholangiocarcinoma. Silver in situ hybridization of MET and HER2 was performed to assess gene amplification. In the entire cancer group, gallbladder, perihilar, and intrahepatic, MET amplification rates were 15.7%, 19.0%, 3.4%, and 14.8%, respectively, and of HER2 amplification rates were 22.4%, 27.2%, 17.2%, and 3.7%, respectively. MET and HER2 protein expressions were significantly correlated with their gene amplification status. RTKs were significantly associated with adverse clinicopathologic features such as advanced pT category and lymph node metastasis. Overall survival was significantly shorter in MET-amplified (P = .024) and EGFR-overexpressed cases (P = .045). Recurrence-free survival was significantly correlated with HER2-amplified (P = .038) and EGFR-overexpressed cases (P = .046) in all patient groups. Overall and recurrence-free survival were significantly shorter in patients who were double positive for HER2 and EGFR. Our data suggested that MET, HER2, and EGFR might be potential therapeutic targets and that their co-expression is a strong prognostic factor for BTCs.

Abstract PO4-26-05: Dual HER2 Testing With Both Immunohistochemistry (IHC) and ISH (In Situ Hybridization): Long Term Analysis of Dual Testing in a Single Academic Institution

Abstract Background: HER-2 critically guides therapies and is prognostic in breast cancer (BC). Current ASCO/CAP guidelines for immunohistochemistry (IHC) define 3+ as positive, 0 and 1+ as negative, and 2+ as equivocal, with additional testing recommended. Current guidelines for in situ hybridization (ISH) define a HER-2/CEP17 ratio of ≥2.0, with an average HER-2 copy number of ≥4.0 signals/cell as ISH positive. With &amp;lt; 4.0 copies HER-2/cell, and for various other ISH groups that are borderline, further specific additional testing is recommended. Data suggest that HER-2 copy number does have clinical relevance in HER-2+ BC, however most clinical trials evaluating HER-2 targeted therapeutics have defined HER-2+ as specifically a HER-2/CEP17 ratio ≥2.0. Limited studies have explored HER-2 copy number and its clinical implication in the HER-2 1+, and 2+ ISH negative population, recently described as HER-2 low. Further, the guidelines for HER-2 testing have changed twice over the past decade, and little is known about the impact of these changes. Design: From 2001- March 2023, all new invasive BC cases tested at University of Vermont (UVM) for HER-2 with both IHC and ISH were analyzed. All testing was performed on formalin-fixed paraffin-embedded tissue, using the HercepTest kit (Dako Corp, Carpinteria, California) (2001-2012) 4B5 Rabbit Monoclonal Antibody (Ventana) (2013-2023) for IHC and the INFORM dual ISH DNA probe (Ventana) for CISH. Interpretation was performed using published criteria at the time of original testing, and all cases with both IHC and CISH testing were independently analyzed by two experienced reviewers. Results: 2734 cases had dual testing with IHC and CISH. 2407 patients (88%) had a HER-2/CEP17 ratio &amp;lt; 2.0, of these, 6.4% had a HER-2 copy number ≥4 and &amp;lt; 6. Only 12% of cases overall had a ratio ≥ 2.0. In IHC 0 and 1+ cases with HER-2/CEP17 ratio of &amp;lt; 2, 0.4% and 4.3% have excess HER-2 copies/cell (defined as ≥ 4), respectively, compared to 13.8% for IHC 2+. For IHC 2+ cases, only 13.6% overall demonstrate amplification, with however, again, an additional 13.8% having excess copy number. Interestingly, 9.6% of the IHC 3+ cases had a ratio of &amp;lt; 2.0, however 50% of those demonstrate HER-2 amplification. Overall, 6.4% of HER-2 non-amplified cases with a ratio &amp;lt; 2.0 have an excess HER-2 copy number. In our full institutional pathology database, 11.2% of cases are HER2+, by either IHC or ISH. Lastly, 43% of cases overall, at UVM, from 2018 – March 2023 would fall into the current classification as HER-2 low (IHC 1+, or IHC 2+ and ISH negative), as well. Additionally, we have evaluated the change in IHC and ISH results that occurred with the changes in the ASCO/CAP guidelines in both 2013 and 2018, further data will be available for presentation. Conclusion: In this large single institutional analysis of dual HER-2 testing, only 12% of cases demonstrate HER-2 amplification, and overall in our institutional pathology database, from 2001 – March 2023, 11.2% of cases are HER-2+ by either IHC or ISH. In our dual tested cohort, only 13.6% of IHC 2+ cases demonstrate amplification, and 13.8% are non-amplified, but have excess HER-2 copy number. We demonstrate a numerical increase in the rate of amplification, and copy number in non-amplified cases, associated with IHC score. In all cases tested with IHC at UVM from 2018 – March 2023, we find 43% of cases meet the current criteria for HER-2 low. Finally, the ASCO/CAP guideline changes from 2013 to 2018 had modest impact on the overall percentage of HER-2+ cases in our series, further data on this impact will be available for presentation. Table. Simultaneously tested IHC and CISH data for new invasive breast cancer cases Citation Format: Xiaocao Xu, Abiy Ambaye, Kara Landry, Peter Kaufman. Dual HER2 Testing With Both Immunohistochemistry (IHC) and ISH (In Situ Hybridization): Long Term Analysis of Dual Testing in a Single Academic Institution [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-26-05.

A system troubleshooting for HIV-1 drug resistance genotyping amplification rate failure at Ethiopian public health institute HIV laboratory

A system troubleshooting for HIV-1 drug resistance genotyping amplification rate failure at Ethiopian public health institute HIV laboratory

The variation and evolution of complete human centromeres

Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.

Drivers of Magnetic Field Amplification at Oblique Shocks: In Situ Observations

Collisionless shocks are ubiquitous structures throughout the Universe. Shock waves in space and astrophysical plasmas convert the energy of a fast-flowing plasma to other forms of energy, including thermal and magnetic energies. Plasma turbulence and high-amplitude electric and magnetic fluctuations are necessary for effective energy conversion and particle acceleration. We survey and characterize in situ observations of reflected ions and magnetic field amplification rates at quasiperpendicular shocks under a wide range of upstream conditions. We report magnetic amplification rates as high as 25 in our current data set. Reflected ions interacting with the incoming plasma create magnetic perturbations that cause magnetic amplification in upstream and downstream regions of quasiperpendicular shocks. Our observations show that, in general, magnetic amplification increases with the fraction of reflected ions, which itself increases with Mach number. Both parameters plateau once full reflection is reached. Magnetic amplification continuously increases with the inverse of the magnetization parameter of the upstream plasma. We find that the extended foot region upstream of shocks and nonlinear processes within that region are key factors for intense magnetic amplification. Our observations at nonrelativistic shocks provide the first experimental evidence that below a certain magnetization threshold, the magnetic amplification efficiency at quasiperpendicular shocks becomes comparable to that at the quasiparallel shocks.