Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.

Reciprocating Oscillation of a Floating Ferrofluid Marble Triggered by Magnetic Fields.

Liquid marbles have the potential for microfluidic transport, medical diagnostics, and chemical analysis due to their negligible stickiness, environmental independence, and excellent mobility. Here, we report a non-contact manipulation strategy to arouse a reciprocating oscillation of ferrofluid marbles floating on the water surface, which can be used as microreactors. We experimentally investigated the quantitative relationship between the oscillation behavior, the applied magnetic field parameters, and the field regulation mechanism. The variables, including the magnetic field strength, marble volume, and switching period, are vital in determining the final state. The oscillation can be separated into three stages: transitional movement, compressive deformation, and rebound, before entering the next cycle. Accordingly, we created a manipulation technique for improving the mixing of inner reactants inside this marble container by remote-controlled shaking after optimizing with an oscillation model.

Comprehensive investigations of near infrared downshift and upconversion luminescence mechanisms in Yb3+ single-doped and Er3+,Yb3+ co-doped SiO2 inverse opals.

Comprehensive investigations of near infrared (NIR) downshift and visible upconversion luminescence (UCL) mechanisms were carried out for Yb3+ single-doped and Er3+,Yb3+ co-doped SiO2 inverse opals under excitation at 256, 378, 520 and 980 nm. NIR emission at 976 nm from the Yb3+-O2- charge transfer state and UCL emission at 500 nm due to the cooperative emission of two Yb3+ ions were observed in SiO2:Yb3+ inverse opal upon excitation at 256 and 980 nm, respectively. The cooperative UCL of two Yb3+ ions was suppressed due to the photon trap created by the photonic band gap. For the SiO2:Er3+,Yb3+ inverse opals, NIR emission of Yb3+ at 976 nm and of Er3+ at 1534 nm were observed upon excitation at 256, 378 and 520 nm, respectively. Upon excitation at 378 and 520 nm, the 976 nm NIR emission of Yb3+ does not arise from (2H11/2/4S3/2) + 2Yb3+(2F7/2) → Er3+(4I15/2) + 2Yb3+(2F5/2) traditional quantum cutting. The NIR emission of Yb3+ at 976 nm may be due to the Er3+(2H11/2) + Yb3+(2F7/2) → Yb3+(2F5/2) + Er3+(4I11/2) cross-relaxation energy transfer process upon excitation at 520 nm. The NIR emission of Yb3+ at 976 nm may arise from the cross-relaxation energy transfer of Er3+(4G11/2) + Yb3+(2F7/2) → Yb3+(2F5/2) + Er3+(4F9/2) and Er3+(4F9/2) + Yb3+(2F7/2) → Yb3+(2F5/2) + Er3+(4I13/2) upon excitation at 378 nm.

Budesonide suspension nebulization treatment in Chinese pediatric patients with cough variant asthma: a multi-center observational study.

OBJECTIVE: To describe the impact of nebulized budesonide inhalation suspension (BIS) on guardian-reported symptoms in Chinese pediatric patients with cough variant asthma (CVA). METHODS: This was a secondary analysis of a prospective, non-interventional study conducted at 39 Chinese sites. Patients with CVA aged ≤5 years were classified according to the severity of baseline symptoms: mild (symptom score ≤3) or severe (symptom score >3). Daytime and night-time symptom scores, disease control, use of bronchodilators, and improvements in symptoms control were compared after 1, 3, 5 and 7 weeks of treatment between groups. RESULTS: Among 914 patients, 821 (89.8%) completed the 7-week treatment. Among all patients, 368 (40.3%) were classified as mild CVA and 529 (57.9%), as severe CVA. Symptom scores in the severe group were higher than those in the mild group at weeks 1, 3, and 5 (p < 0.05), but not at week 7 (p > 0.05). Further, more patients in the mild group achieved disease control at any time point (98.6% at 3 weeks and 99.7% at 7 weeks), compared with the patients in the severe group (p < 0.001). The proportion of patients requiring bronchodilators differed between the groups until week 5 (p < 0.001). No severe or drug-related adverse events were reported. CONCLUSIONS: Individualized BIS treatment should be formulated according to the severity of baseline symptoms in CVA patients. Patients with mild CVA showed improvement after a shorter treatment time, while patients with severe CVA might require a longer time to respond to the treatment.

Follicular hyperandrogenism downregulates aromatase in luteinized granulosa cells in polycystic ovary syndrome women.

Women with polycystic ovary syndrome (PCOS) undergoing IVF-embryo transfer based-assisted reproductive technology (ART) treatment show variable ovarian responses to exogenous FSH administration. For better understanding and control of PCOS ovarian responses in ART, the present study was carried out to compare the follicular hormones and the expression of granulosa cell genes between PCOS and non-PCOS women during ART treatment as well as their IVF outcomes. Overall, 138 PCOS and 78 non-PCOS women were recruited for the present study. Follicular fluid collected from PCOS women showed high levels of testosterone. The expression of aromatase was found significantly reduced in luteinized granulosa cells from PCOS women. In cultured luteinized granulosa cells isolated from non-PCOS women, their exposure to testosterone at a level that was observed in PCOS follicles could decrease both mRNA and protein levels of aromatase in vitro. The inhibitory effect of testosterone was abolished by androgen receptor antagonist, flutamide. These results suggest that the hyperandrogenic follicular environment may be a key hazardous factor leading to the down-regulation of aromatase in PCOS.

A prostate seed implantation robot system based on human-computer interactions: Augmented reality and voice control.

The technology of robot-assisted prostate seed implantation has developed rapidly. However, during the process, there are some problems to be solved, such as non-intuitive visualization effects and complicated robot control. To improve the intelligence and visualization of the operation process, a voice control technology of prostate seed implantation robot in augmented reality environment was proposed. Initially, the MRI image of the prostate was denoised and segmented. The three-dimensional model of prostate and its surrounding tissues was reconstructed by surface rendering technology. Combined with holographic application program, the augmented reality system of prostate seed implantation was built. An improved singular value decomposition three-dimensional registration algorithm based on iterative closest point was proposed, and the results of three-dimensional registration experiments verified that the algorithm could effectively improve the three-dimensional registration accuracy. A fusion algorithm based on spectral subtraction and BP neural network was proposed. The experimental results showed that the average delay of the fusion algorithm was 1.314 s, and the overall response time of the integrated system was 1.5 s. The fusion algorithm could effectively improve the reliability of the voice control system, and the integrated system could meet the responsiveness requirements of prostate seed implantation.

Arthroscopic treatment for rotator cuff injury and frozen shoulder with concomitant rotator cuff injury: analysis of efficacy and factors influencing prognosis.

OBJECTIVE: To analyze the efficacy of arthroscopic treatment for patients with rotator cuff injuries and frozen shoulder combined with rotator cuff injuries and assess the factors influencing patient prognosis. METHODS: A retrospective analysis was performed on 85 patients who underwent arthroscopic surgery at Hanzhong Central Hospital between October 2016 and October 2021, including 42 patients treated for rotator cuff injuries alone (Group A), and 43 patients for frozen shoulder combined with rotator cuff injuries (Group B). Both groups underwent general anesthesia with controlled hypotension during surgery. Treatment outcomes, including shoulder joint functional scores, pain scores, shoulder joint range of motion, and muscle strength were assessed and compared between the two groups before treatment, as well as at 2 weeks and 2 months post-treatment. Quality of life was also evaluated and compared at 2 months post-treatment. Patients were categorized into good and poor prognosis groups based on their outcome, and factors influencing patient prognosis were analyzed. RESULTS: Before treatment, both groups exhibited relatively low shoulder joint function scores and external rotation angles, coupled with higher pain scores; however, these differences were not significant between groups (all P>0.05). The surgery duration for Group B was notably longer than that of Group A (P<0.05). Nevertheless, there was no significant variance in intraoperative blood loss between the two groups (P>0.05). After a 2-week treatment duration, both groups demonstrated a significant improvement in shoulder joint function score, pain score, and shoulder joint range of motion compared to baseline, but with no statistically significant intergroup differences. However, two months after the treatment, patients in Group A exhibited marked improvements in shoulder joint function score, pain score, shoulder joint range of motion, and overall quality of life compared to Group B (all P<0.05). Furthermore, the therapeutic efficacy in Group A was superior to that in Group B at the 2-month follow-up (P<0.05). Age, comorbid diabetes, metabolic disorders such as thyroid dysfunction, and the extent of shoulder cuff injury were identified as independent risk factors influencing prognosis. CONCLUSION: Arthroscopic treatment is effective for both frozen shoulder combined with rotator cuff injury and rotator cuff injury alone, with better outcomes observed in patients with rotator cuff injury only. This technique warrants further promotion.

Demagnetization Parameters Evaluation of Magnetic Shields Based on Anhysteretic Magnetization Curve.

To achieve the nearly zero-field environment, demagnetization is an indispensable step for magnetic shields composed of high-permeability material, which adjusts the magnetization of the material to establish magnetic equilibrium with the environmental field and improve the shielding performance. The ideal demagnetization can make the high-permeability material on the anhysteretic magnetization curve to have a higher permeability than on the initial magnetization curve. However, inappropriate parameters of degaussing field cause the magnetization state to deviate from the anhysteretic magnetization curve. Therefore, this article proposes a new assessment criterion to analyze and evaluate the parameters of degaussing field based on the difference between the final magnetization state after demagnetization and theoretical anhysteretic state of the shielding material. By this way, the magnetization states after demagnetizations with different initial amplitude, frequency, period number and envelope attenuation function are calculated based on the dynamic Jiles-Atherton (J-A) model, and their magnetization curves under these demagnetization conditions are also measured and compared, respectively. The lower frequency, appropriate amplitude, sufficient period number and logarithmic envelope attenuation function can make the magnetization state after demagnetization closer to the ideal value, which is also consistent with the static magnetic-shielding performance of a booth-type magnetically shielded room (MSR) under different demagnetization condition.

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.

Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable wet lab and computational protocol for Oxford Nanopore Technologies (ONT) long-read sequencing that seeks to provide a genuine alternative to short-reads for large-scale genomics projects. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the NIH Center for Alzheimer's and Related Dementias (CARD). Using a single PromethION flow cell, we can detect SNPs with F1-score better than Illumina short-read sequencing. Small indel calling remains to be difficult inside homopolymers and tandem repeats, but is comparable to Illumina calls elsewhere. Further, we can discover structural variants with F1-score comparable to state-of the-art methods involving Pacific Biosciences HiFi sequencing and trio information (but at a lower cost and greater throughput). Using ONT based phasing, we can then combine and phase small and structural variants at megabase scales. Our protocol also produces highly accurate, haplotype-specific methylation calls. Overall, this makes large-scale long-read sequencing projects feasible; the protocol is currently being used to sequence thousands of brain-based genomes as a part of the NIH CARD initiative. We provide the protocol and software as open-source integrated pipelines for generating phased variant calls and assemblies.

Structural variation across 138,134 samples in the TOPMed consortium.

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hemotologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

Structural variation across 138,134 samples in the TOPMed consortium.

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

TT-Mars: structural variants assessment based on haplotype-resolved assemblies.

Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for example, when different alignment scoring metrics provide equally supported but different variant calls on the same data. Here, we provide an alternative approach, TT-Mars, that takes advantage of the recent production of high-quality haplotype-resolved genome assemblies by providing false discovery rates for variant calls based on how well their call reflects the content of the assembly, rather than comparing calls themselves.

Comparisons of recurrence-free survival and overall survival between microwave versus radiofrequency ablation treatment for hepatocellular carcinoma: A multiple centers retrospective cohort study with propensity score matching.

Both microwave (MW) ablation and radiofrequency (RF) ablation are widely used for hepatocellular carcinoma (HCC) treatments in clinic. However, it is still unclear if ablative methods could influence the recurrence-free survival (RFS) and overall survival (OS) of HCC patients. Therefore, we carried out this multi-center retrospective cohort study to investigate the differences of recurrence-free survival (RFS) and overall survival (OS) between MW ablation and RF ablation by survival analysis. From January 2014 to December 2016, patients who received thermal ablation surgery for HCC treatment were screened. Finally, 452 patients met the eligibility criteria and finished the follow-up. Univariable and multivariable regression analyses were used to identify independent predictive factors of the RFS and OS. Also, propensity score matching (PSM) was used to balance the bias between two groups. Finally, we found that before the PSM, the univariable and multivariable regression analyses revealed that there were no significant differences on the RFS between two groups. Same results were obtained for the OS. After PSM, 115 pairs of patients were created, and both the univariable and multivariable regression analyses suggested that there were still no significant differences on the RFS between two groups. Same results were obtained for the OS. In conclusion, our present study showed that there were no significant differences between MW ablation and RF ablation for HCC patients on the RFS or OS.

Effects of chromosome 9 inversion on IVF/ICSI: A 7-year retrospective cohort study.

BACKGROUND: This study focused on the outcomes of patients with pericentric inversion of chromosome 9 who underwent IVF/ICSI and fresh day 2 or day 3 embryo transfer and the possible impacts of carrier gender and chromosome karyotype on pregnancy outcomes. METHODS: A total of 214 couples (107 couples with one pericentric inversion of chromosome 9 in one partner [Group 1], 107 couples with normal karyotypes [Group 2]) underwent their first IVF/ICSI treatment and were included in this study. Oocyte number, normal fertilization rates, abnormal fertilization rates, cleavage rates, embryo utilization rates, fresh embryo transfer rates, clinical pregnancy rates (CPR), implantation rates, miscarriage rates, and live birth rates per embryo transfer (LBR) were compared between groups. RESULTS: Group 1 did not show any disadvantage when compared with Group 2. The CPR and LBR were similar between all groups. The female carrier group had a higher normal fertilization rate and higher utilization rate than the male carrier group. Cases with inv(9)(p12;q13) had a lower utilization rate but a higher implantation rate than the remaining karyotypes. CONCLUSION: In the first IVF or ICSI cycle, couples with one pericentric inversion of chromosome 9 in one partner had satisfactory outcomes. The subgroup analysis showed a tendency of better prognosis for the female carrier and inv(9)(p12;q13) type.

Effects of Adenovirus-Mediated Hepatocyte Growth Factor Gene Therapy on Postinfarct Heart Function: Comparison of Single and Repeated Injections.

Clinical trials testing the effects of a single injection of adenovirus carrying the human hepatocyte growth factor gene (Ad-HGF) in patients with chronic ischemic heart failure failed to show consistent improvements in cardiac function. The aim of this study was to evaluate the efficacy of repeated injections of Ad-HGF in a rat model of postinfarct heart failure. Ad-HGF or Ad-green fluorescent protein (GFP) was administered to Sprague Dawley rat models of postinfarct heart failure via single or fractional repeated intrapericardial injection. Heart function was monitored by magnetic resonance imaging for 4 and 8 weeks after injections. The expression of HGF or factor VIII/Ki-67 was evaluated by Western blot assay or immunofluorescence. We found that Ad-HGF gene expression could be prolonged in vivo by repeated injections and that cardiac function was significantly improved in the Ad-HGF repeat-injection group compared with the Ad-HGF single-injection group. Newly formed capillary density was similarly higher in the Ad-HGF repeat-injection group compared with that in the Ad-HGF single-injection group. We therefore conclude that fractional repeated injections of Ad-HGF may represent a promising therapeutic strategy to improve cardiac function in the setting of postinfarct heart failure.

Coupling of Ag Nanoparticle with Inverse Opal Photonic Crystals as a Novel Strategy for Upconversion Emission Enhancement of NaYF4: Yb(3+), Er(3+) Nanoparticles.

Rare-earth-ion-doped upconversion (UC) nanoparticles have generated considerable interest because of their potential application in solar cells, biological labeling, therapeutics, and imaging. However, the applications of UC nanoparticles were still limited because of their low emission efficiency. Photonic crystals and noble metal nanoparticles are applied extensively to enhance the UC emission of rare earth ions. In the present work, a novel substrate consisting of inverse opal photonic crystals and Ag nanoparticles was prepared by the template-assisted method, which was used to enhance the UC emission of NaYF4: Yb(3+), Er(3+) nanoparticles. The red or green UC emissions of NaYF4: Yb(3+), Er(3+) nanoparticles were selectively enhanced on the inverse opal substrates because of the Bragg reflection of the photonic band gap. Additionally, the UC emission enhancement of NaYF4: Yb(3+), Er(3+) nanoparticles induced by the coupling of metal nanoparticle plasmons and photonic crystal effects was realized on the Ag nanoparticles included in the inverse opal substrate. The present results demonstrated that coupling of Ag nanoparticle with inverse opal photonic crystals provides a useful strategy to enhance UC emission of rare-earth-ion-doped nanoparticles.

Recovery of HPA Axis Function After Successful Gonadotropin-Induced Pregnancy and Delivery in a Woman With Panhypopituitarism: Case Report and Review.

Hypopituitarism is defined as the partial or complete defect of anterior pituitary hormone secretion. Patients with hypopituitarism usually need life-long hormone replacement therapy. However, in this case, we report a patient with panhypopituitarism whose hypothalamus-pituitary-adrenal (HPA) axis function was completely recovered after pregnancy and delivery. In this case study, we reported the case management and conducted a review of literature to identify the possible mechanism of pituitary function recovery. The patient who suffered from secondary amenorrhea was found a nonfunctioning pituitary macroadenoma, and the hormone test showed serum cortisol, FT3, FT4, thyrotropic hormone, and prolactin were at normal range. After surgical removal of the tumor which invasion in the sellar region, the patient had panhypopituitarism confirmed by the routine hormone test. Though spontaneous pregnancy is impossible in female patients with panhypopituitarism, the patient was restored fertility by the help of artificial reproductive techniques. After the confirmation of the pregnancy, levothyroixine was increased to 75 µg daily and readjusted to 150 µg daily before delivery according to the monthly measurement thyroid function. Hydrocortisone 10 mg daily replaced cortisone acetate; the dose was increased according to the symptoms of morning sickness. A single stress dose of hydrocortisone (200 mg) was used before elective cesarean delivery and was tapered to the dose of 10 mg per day in 1 week. Levothyroixine was reduced to 75 µg daily after delivery. During follow-up, her hypothalamus-pituitary-adrenal (HPA) axis function was completely recovered. The peak serum cortisol level could increase to 19.08 µg/dL by insulin-induced hypoglycemia. However, growth hormone remained unresponsive to the insulin-tolerance test, and thyroid hormone still needed exogenous supplementation. Hormone replacement therapy needed closely followed by endocrinologist and multidisciplinary cooperation during the pregnancy of patients with hypopituitarism. This case indicates that the pituitary function may partially recover after pregnancy in panhypopituitarism patients.