Search

Deep learning (DL) algorithms are used to diagnose diabetic retinopathy (DR). However, most of these algorithms have been trained using global data or data from patients of a single region. Using different model architectures (e.g., Inception-v3, ResNet101, and DenseNet121), we assessed the necessity of modifying the algorithms for universal society screening. We used the open-source dataset from the Kaggle Diabetic Retinopathy Detection competition to develop a model for the detection of DR severity. We used a local dataset from Taipei City Hospital to verify the necessity of model localization and validated the three aforementioned models with local datasets. The experimental results revealed that Inception-v3 outperformed ResNet101 and DenseNet121 with a foreign global dataset, whereas DenseNet121 outperformed Inception-v3 and ResNet101 with the local dataset. The quadratic weighted kappa score (κ) was used to evaluate the model performance. All models had 5–8% higher κ for the local dataset than for the foreign dataset. Confusion matrix analysis revealed that, compared with the local ophthalmologists’ diagnoses, the severity predicted by the three models was overestimated. Thus, DL algorithms using artificial intelligence based on global data must be locally modified to ensure the applicability of a well-trained model to make diagnoses in clinical environments.

Quinclorac (QNC) is a highly selective, hormonal, and low-toxic herbicide with a long duration. And the growth and development of subsequent crops are easily affected by QNC accumulated in the soil. In this paper, a QNC-degrading strain D was isolated and screened from the rice paddy soil. Through morphology, physiological and biochemical tests and 16Sr DNA gene analysis, strain D was identified asCellulosimicrobium cellulanssp. And the QNC degradation characteristics of strain D were studied. Under the optimal culture conditions, the QNC-degrading rate was 45.9% after culturing for 21 days. The QNC-degrading efficiency of strain D in the field was evaluated by a simulated pot experiment. The results show that strain D can promote the growth of rice and QNC-degrading effectively. This research could provide a new bacterial species for microbial degradation of QNC and lay a theoretical foundation for further research on QNC remediation.ImportanceAt present, some QNC-degrading bacteria have been isolated from different environments, but there are no reports ofCellulosimicrobium cellulanssp. bacterial that could degrade QNC. In this study, a new QNC-degradation strain was selected from the paddy soil. The degradation characteristics of strain D were studied in detail. The results shown that strain D had a satisfactory quinclorac-degrading efficiency. Two degradation products of QNC by strain D were identified by HPLC-Q-TOF/MS: 3-pyridylacetic acid (138.0548 m/z) and 3-ethylpyridine (108.0805 m/z), which have not been reported before. The strain D had a potential ability of quinclorac-degrading effectively in the quinclorac-polluted paddy field environment.

While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.

Hi-Culfite, a protocol combining Hi-C and whole-genome bisulfite sequencing (WGBS), determines chromatin contacts and DNA methylation simultaneously. Hi-Culfite also reveals relationships that cannot be seen when the two assays are performed separately. For instance, we show that loci associated with open chromatin exhibit context-sensitive methylation: when their spatial neighbors lie in closed chromatin, they are much more likely to be methylated.

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4 + T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.

// Mau-Shin Chi 1, 3 , Cheng-Yen Lee 1 , Su-Chen Huang 1 , Kai-Lin Yang 1 , Hui-Ling Ko 1 , Yen-Kung Chen 2 , Chen-Han Chung 3 , Kuang-Wen Liao 3 , Kwan-Hwa Chi 1, 4 1 Department of Radiation Therapy and Oncology, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan 2 Department of Nuclear Medicine and PET Center, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan 3 Institue of Molecular Medicine and Bioengineering, National Chiao-Tung University, Hsinchu, Taiwan 4 School of Medicine and Institute of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan Correspondence to: Kwan-Hwa Chi, e-mail: M006565@ms.skh.org.tw Keywords: hydroxychloroquine, sirolimus, soft tissue sarcoma Received: April 21, 2015 Accepted: August 26, 2015 Published: September 07, 2015 ABSTRACT Rationale: According to the metabolic symbiosis model, cancer stromal fibroblasts could be hijacked by surrounding cancer cells into a state of autophagy with aerobic glycolysis to help provide recycled nutrients. The purpose of this study was to investigate whether combined treatment with the autophagy inhibitor: hydroxychloroquine (HCQ) and the autophagy inducer: sirolimus (rapamycin, Rapa) would reduce glucose utilization in sarcoma patients. Methods: Ten sarcoma patients who failed first-line treatment were enrolled in this study. They were treated with 1 mg of Rapa and 200 mg of HCQ twice daily for two weeks. The standardized uptake values (SUV) from pretreatment and posttreatment [18F]-fluorodeoxyglucose positron emission tomography (FDG PET) scans were reviewed, and changes from the baseline SUVmax were evaluated. Results: Based on FDG PET response criteria, six patients had a partial response; three had stable disease, and one had progressive disease. Nevertheless, none of them showed a reduction in tumor volume. The mean SUVmax reduction in the 34 lesions evaluated was − 19.6% (95% CI = −30.1% to −9.1%), while the mean volume change was +16.4% (95% CI = +5.8% to + 27%). Only grade 1 toxicities were observed. Elevated serum levels of lactate dehydrogenase were detected after treatment in most metabolic responders. Conclusions: The results of reduced SUVmax without tumor volume reduction after two weeks of Rapa and HCQ treatment may indicate that non-proliferative glycolysis occurred mainly in the cancer associated fibroblast compartment, and decreased glycolytic activity was evident from Rapa + HCQ double autophagy modulator treatment.

We show that when it takes time for a durable goods monopolist to make its high-end new technology accessible to low-end market (the trickle-down technology constraint), the monopolist's high-end product might have a higher-than-optimum quality. This result differs from conventional screening models, in which the qualities of non-durable goods supplied by a monopolist never exceed the optimum, and only consumers with the highest valuation consume the efficient quality. In another literature discussing a durable goods monopolist who delays the introduction of low-end product as a marketing strategy, but not due to the trickle-down constraint, the qualities will not exceed the optimum either. Our results show that the trickle-down constraint will make the monopolist chooses a higher-than-optimum quality when the difference of the valuations of high demand and low demand consumers are in certain ranges. The intuition follows Spence (1975): the efficient quality is determined by the marginal cost and the average of all consumers’ marginal valuations, while the monopolist chooses quality such that the marginal cost equals the marginal consumer’s marginal valuation.

The human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci—almost always bound by CTCF and cohesin—lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid. Mapping the nucleome in 4D during cohesin loss and recovery reveals that cohesin degradation eliminates loop domains but has only modest transcriptional consequences. Keywords: cohesion; genome architecture; loop extrusion; chromatin loops; superenhancers; gene regulation; nuclear compartments; Hi-C; 4D Nucleome; CTCF

SUMMARYThe human genome folds to create thousands of intervals, called “contact domains,” that exhibit enhanced contact frequency within themselves. “Loop domains” form because of tethering between two loci - almost always bound by CTCF and cohesin – lying on the same chromosome. “Compartment domains” form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loci in different compartments that had been in the same loop domain become more segregated. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. Cohesin restoration quickly reverses these effects, consistent with a model where loop extrusion is rapid.

Purpose To investigate serum markers associated with radiation pneumonitis (RP) grade ≥3 in patients with lung cancer who were treated with radiation therapy. Methods and Materials Pretreatment serum samples from patients with stage Ib-IV lung cancer who developed RP within 1 year after radiation therapy were analyzed to identify a proteome marker able to stratify patients prone to develop severe RP by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Dosimetric parameters and 3 biological factors were compared. Results Serum samples from 16 patients (28%) with severe RP (grade 3-4) and 42 patients (72%) with no or mild RP (grade 0-2) were collected for analysis. All patients received a median of 54 Gy (range, 42-70 Gy) of three-dimensional conformal radiation therapy with a mean lung dose (MLD) of 1502 cGy (range, 700-2794 cGy). An m/z peak of 11,480 Da was identified by SELDI-TOF-MS, and serum amyloid A (SAA) was the primary splitter serum marker. The receiver operating characteristic area under the curve of SAA (0.94; 95% confidence interval [CI], 0.87-1.00) was higher than those of C-reactive protein (0.83; 95% CI, 0.72-0.94), interleukin-6 (0.79; 95% CI, 0.65-0.94), and MLD (0.57; 95% CI, 0.37-0.77). The best sensitivity and specificity of combined SAA and MLD for predicting RP were 88.9% and 96.0%, respectively. Conclusions Baseline SAA could be used as an auxiliary marker for predicting severe RP. Extreme care should be taken to limit the lung irradiation dose in patients with high SAA.

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) and RNA-seq profiles from activated CD4+ T cells of up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, in patterns consistent with the 3D organization of chromosomes measured by in situ Hi-C in T cells. 15% of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak through disrupting binding sites for transcription factors important for T cell differentiation and activation. These ATAC quantitative trait nucleotides (ATAC-QTNs) have the largest effects on co-accessible peaks, are associated with gene expression from the same aliquot of cells, are rarely affecting core binding motifs, and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis- regulatory elements, in isolation or in concert, to influence gene expression in primary immune cells that play a key role in many human diseases.

During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called “superloops.” DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.

We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

Oral Diseases (2012) 18, 809–815 Objective: The infection of human papilloma virus (HPV) has been reported in head and neck cancer; however, the clinical significance of HPV infection on the pathogenesis of oral cavity squamous cell carcinoma (OSCC) is still uncertain. Materials and Methods: The study recruited 103 patients with pathological early-stage OSCC between March 1997 and December 2003 from Chang Gung Memorial Hospital, Taiwan. Tumor specimens were HPV-genotyped by the EasychipVR HPV Blot method. Clinical association study was performed by using chi-square, Kaplan–Meier, and logrank tests. Results: Thirty-one patients (30.1%) were positive for HPV infection. The most frequent HPV types were types 16 (16 patients, 51.6%) and 18 (seven patients, 22.6%). HPV infection was not associated with tumor aggressiveness (pathological tumor stage or differentiation status), risk exposure (alcohol, cigarette, or areca quid chewing habit), or the treatment outcome (disease-free survival or overall survival). However, infection with HPV-18 was associated with the occurrence of a second primary cancers (P = 0.033), indicating the infection of HPV in OSCC enhances the susceptibility of developing secondary malignancy. Conclusions: There are 30% of the patients with OSCC infected with HPV, with most high-risk types. HPV-18 infection may enhance the susceptibility of second primary tumors. Large scale of validation study will be needed to confirm this result.

Metal sludge from industrial wastewater treatment plants was mixed with mining residues to be recycled into lightweight aggregate (LWA) through sintering at different temperatures. The physical properties of the LWA thus obtained were examined by scanning electron microscopy analyzer (SEM) coupled with an energy dispersive X-ray analyzer (EDX). The sequential extraction method combined with inductively coupled plasma atomic emission spectrometry (ICP-AES) was employed to determine the concentration and distribution of hazardous toxic elements in the metal sludge-based artificial LWA. The results show that the leaching concentrations of Cd, Cr, Cu, and Pb present in the non-sintered raw aggregate pellets reached 7.4, 68.0, 96.0, and 61.4 mg/l, respectively, far exceeding the regulatory threshold. Sintering at 1150 degrees C for 15 min results in stronger chemical bonds being formed between the elements. Hence, after the first three steps of sequential extraction, the concentrations of Cr, Cu, and Pb reached 2.69, 1.50, and 1.88 mg/l at 1150 degrees C, while the final residues had total concentrations of 96.1, 88.4, and 60.6 mg/kg, respectively, with Cd undetected in both phases. The concentration levels fell within the regulatory threshold, indicating that the LWA fabricated from recycled metal sludge contains elements that are toxic and hazardous but not leached. Having no harmful effect on the environment, the metal sludge-based artificial LWA is not only safe but also practical with good physical properties.

In this study, artificial lightweight aggregate (LWA) manufactured from recycled resources was investigated. Residues from mining, fly ash from an incinerator and heavy metal sludge from an electronic waste water plant were mixed into raw aggregate pellets and fed into a tunnel kiln to be sintered and finally cooled rapidly. Various feeding and sintering temperatures were employed to examine their impact on the extent of vitrification on the aggregate surface. Microstructural analysis and toxicity characteristic leaching procedure (TCLP) were also performed. The results show that the optimum condition of LWA fabrication is sintering at 1150 degrees C for 15 min with raw aggregate pellets fed at 750 degrees C. The rapidly vitrified surface envelops the gas produced with the increase in internal temperature and cooling by spraying water prevents the aggregates from binding together, thus forming LWA with specific gravity of 0.6. LWA produced by sintering in tunnel kiln shows good vitrified surface, low water absorption rate below 5%, and low cylindrical compressive strength of 4.3 MPa. In addition, only trace amounts of heavy metals were detected, making the LWA non-hazardous for construction use.

We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigenetic accessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomain clusters decompact into mononucleosome fibers through a mechanism that requires Myc and continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATP production. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.

Electronic word of mouth (eWOM) has been an important factor influencing consumer purchase decisions. Using the ABC model of attitude, this study proposes a model to explain how eWOM affects online discussion forums. Specifically, we propose that platform (Web site reputation and source credibility) and customer (obtaining buying-related information and social orientation through information) factors influence purchase intentions via perceived positive eWOM review credibility, as well as product and Web site attitudes in an online community context. A total of 353 online discussion forum users in an online community (Fashion Guide) in Taiwan were recruited, and structural equation modeling (SEM) was used to test the research hypotheses. The results indicate that Web site reputation, source credibility, obtaining buying-related information, and social orientation through information positively influence perceived positive eWOM review credibility. In turn, perceived positive eWOM review credibility directly influences purchase intentions and also indirectly influences purchase intentions via product and Web site attitudes. Finally, we discuss the theoretical and managerial implications of the findings.

Procalcitonin (PCT) is expressed in nonthryoidal tissues of humans during severe infections. Serum PCT levels are measured to diagnose and guide therapy, and there is some evidence that PCT may also contribute to the pathogenesis of sepsis. We tested whether disruption of the gene encoding PCT in mice affected the course of sepsis. Mice with exons 2–5 of the gene encoding calcitonin/calcitonin gene–related polypeptide α (Calca) knocked out and congenic C57BL/6J control mice were challenged with aerosolized Streptococcus pneumoniae or Pseudomonas aeruginosa, or injected intraperitoneally with S. pneumoniae. There were no significant differences in the survival of knockout and control mice in the two pneumonia models, and no significant differences in weight loss, splenic bacterial counts, or blood leukocyte levels in the peritoneal sepsis model. To verify disruption of the Calca gene in knockout mice, the absence of calcitonin in the serum of knockout mice and its presence and inducibility in control mice were confirmed. To evaluate PCT expression in nonthyroidal tissues of control mice, transcripts were measured in multiple organs. PCT transcripts were not significantly expressed in liver or spleen of control mice challenged with aerosolized P. aeruginosa or intraperitoneal endotoxin, and were expressed in lung only at low levels, even though serum IL-6 rose 3,548-fold. We conclude that mice are not an ideal loss-of-function model to test the role of PCT in the pathogenesis of sepsis because of low nonendocrine PCT expression during infection and inflammation. Nonetheless, our studies demonstrate that nonendocrine PCT expression is not necessary for adverse outcomes from sepsis.

The tumor microenvironment is a key determinant for radio-responsiveness. Immune cells play an important role in shaping tumor microenvironments; however, there is limited understanding of how natural killer (NK) cells can enhance radiation effects. This study aimed to assess the mechanism of reciprocal complementation of radiation and NK cells on tumor killing. Various tumor cell lines were co-cultured with human primary NK cells or NK cell line (NK-92) for short periods and then exposed to irradiation. Cell proliferation, apoptosis and transwell assays were performed to assess apoptotic efficacy and cell viability. Western blot analysis and immunoprecipitation methods were used to determine XIAP (X-linked inhibitor of apoptosis protein) and Smac (second mitochondria-derived activator of caspase) expression and interaction in tumor cells. Co-culture did not induce apoptosis in tumor cells, but a time- and dose-dependent enhancing effect was found when co-cultured cells were irradiated. A key role for caspase activation via perforin/granzyme B (Grz B) after cell-cell contact was determined, as the primary radiation enhancing effect. The efficacy of NK cell killing was attenuated by upregulation of XIAP to bind caspase-3 in tumor cells to escape apoptosis. Knockdown of XIAP effectively potentiated NK cell-mediated apoptosis. Radiation induced Smac released from mitochondria and neutralized XIAP and therefore increased the NK killing. Our findings suggest NK cells in tumor microenvironment have direct radiosensitization effect through Grz B injection while radiation enhances NK cytotoxicity through triggering Smac release.

DNA methylation is a critical regulator of cis-regulatory elements that can impact the distribution of epigenetic regulators and transcription factors. We have mapped DNA methylation changes in human CD34+ cells and downstream progeny to detect changes in DNA methylation with differentiation. Some large regions of low DNA methylation emerge with differentiation, which we call dynamic (d-) canyons. In order to determine whether these correlate with changes in the 3D genome, we generated 6 high-resolution Hi-C contact maps from CD34+CD38- cells, Adult bone marrow CD34+ cells, 7 days cultured CD34+ cells, CD71+CD36+CD235+ Erythroid cells, CD4+ T cells and AML patient blast cells. We generated ~ 1 billion mapped reads in order to create each 3D map of the genome at kilobase resolution. We identified several sites of d-canyons which correlate with changes in Hi-C loops. To study the functional role of d-canyons, we performed CRISPR/CAS9 mediated genome engineering targeting three sites of interest in CD34+ progenitors. We designed sgRNAs to delete several d-canyon regions that exhibited cell-type specific methylation and dynamic H3K27ac marking. First, we targeted a novel putative regulatory region of the RUNX1 gene, a critical master regulator of hematopoiesis that is frequently mutated in human leukemia. From genome-wide DNA methylation profiling, we identified a d-canyon located in the first intron of RUNX1, which overlaped with a H3K27ac peak in human CD34+CD38- hematopoietic progenitor cells. DNA methylation in this region is further depleted in T cells and increased in AML cells, suggesting a role for regulating RUNX1 in specific cell types. To study its function, we designed 2 sgRNAs to delete a 1.8 kb d-canyon. CRISPR/Cas9-mediated deletion of this region resulted in ablation of RUNX1 expression in cord blood hematopoietic stem cells and a significant decrease of engraftment activity in NSG mice along with an increase of erythroid colony forming ability in in vitro assays. In addition, we identified d-canyons upstream of the master regulators GATA2 and in the HOXA cluster. We deleted 1.7kb d-canyon upstream of GATA2 gene, finding that it resulted in increased self-renewal of CD34+CD38- cells in NSG xenografts. In contrast, when we deleted one a d-canyon located ~2Mb upstream of the HOXA cluster, within a HiC loop signal present only in CD34+CD38- cells, we observed in decreased CD34+CD38- cell self-renewal but a significant increase of CD34+CD38+ differentiated progenitors in an in vitro culture system, as well as in NSG mice. Colony forming assay showed decreased colony size and numbers. Finally, we identified a d-canyon associated with TCF3, also known as E2A, a transcription factor involved in B and T cell lineage differentiation. We designed 4 sgRNAs to delete 1.5kb d-canyon edge regions within the second intron of TCF3. Removal of this region resulted in a significant decrease of CD19+ B cells, but an increase of CD3+ T cells in NSG mice. Taken together, these results suggest the functional importance of d-canyons for orchestrating genome architecture and fate decisions of hematopoietic stem cells. These findings advance our understanding of the relationship between DNA methylation changes and loop interactions, providing new insights into the potential impact of potential aberrant DNA methylation and chromatin structure. Disclosures No relevant conflicts of interest to declare.

Local radiotherapy (RT) plus intratumoral dendritic cell (DC) injection can mediate immunological response. We hypothesized that co-injection of exogenous recombinant heat shock protein 70 (rHsp70) in combination with RT-DC could be as effective as co-injection of HSP-peptide for evoking specific immune response. rHsp70-prostate-specific antigen (rHSP70C'-PSA) and alpha-fetoprotein (rHSP70C'-AFP) were used to compare specific response. Growth inhibition of the tumor and the systemic anti-tumor immune response were measured on CT26/PSA and CT26/AFP mice model. Intratumoral co-injection of rHsp70 and DC into the irradiated tumor site induced a more potent anti-tumor immune response than injection of DC alone. rHsp70 was as effective as rHsp70C'-PSA or rHsp70C'-AFP in inducing a tumor-specific cytotoxic T lymphocyte response or tumor growth delay. These results demonstrate that co-administration with rHsp70 and radiotherapy could be a simple and effective source of tumor antigens to achieve RT-DC immunotherapy protocol and easy to apply in clinical use.

Foundry engineering can not only produce precise one-piece and complex parts, but can also conserve materials, which is why the industrial market is happy to adopt it. The most dangerous step in the foundry process is the pouring process. This article focuses on this pouring process, which may cause serious safety hazards, and employs Substance-Field Analysis and Contradiction Analysis from the Theory of Inventive Problem-Solving (TRIZ) to seek solutions and improved methods for lowering hazard potential, ensuring factory safety, raising productivity, and promoting workers' welfare.

Background Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS) is a frequently used technique for cancer biomarker research. The specificity of biomarkers detected by SELDI can be influenced by concomitant inflammation. This study aimed to increase detection accuracy using a two-stage analysis process. Methods Sera from 118 lung cancer patients, 72 healthy individuals, and 31 patients with inflammatory disease were randomly divided into training and testing groups by 3:2 ratio. In the training group, the traditional method of using SELDI profile analysis to directly distinguish lung cancer patients from sera was used. The two-stage analysis of distinguishing the healthy people and non-healthy patients (1st-stage) and then differentiating cancer patients from inflammatory disease patients (2nd-stage) to minimize the influence of inflammation was validated in the test group. Results In the test group, the one-stage method had 87.2% sensitivity, 37.5% specificity, and 64.4% accuracy. The two-stage method had lower sensitivity (> 70.1%) but statistically higher specificity (80%) and accuracy (74.7%). The predominantly expressed protein peak at 11480 Da was the primary splitter regardless of one- or two-stage analysis. This peak was suspected to be SAA (Serum Amyloid A) due to the similar m/z countered around this area. This hypothesis was further tested using an SAA ELISA assay. Conclusions Inflammatory disease can severely interfere with the detection accuracy of SELDI profiles for lung cancer. Using a two-stage training process will improve the specificity and accuracy of detecting lung cancer.

One of the most popular issues in electrostatic biology is the effects of a high-voltage electrostatic field (HVEF) on the thawing of chicken thigh meat. In this study, chicken thigh meat was treated with HVEF (E-group), and compared to samples stored in a common refrigerator (R-group), to investigate how HVEF affects chicken thigh meat quality after thawing at low temperature storage (-3 and 4 degrees C). The results showed that there were no significant differences in biochemical and microorganism indices at -3 degrees C. However, the HVEF can significantly shorten thawing time for frozen chicken thigh meat at -3 degrees C. After thawing chicken thigh meat and storing at 4 degrees C, the total viable counts reached the Intl. Commission on Microbiological Specification for Foods limit of 10(7) CFU/g on the 6 and 8 d for the R- and E-group, respectively. On the 8th d, the volatile basic nitrogen had increased from 11.24 mg/100 g to 21.9 mg/100 g for the E-group and 39.9 mg/100 g for the R-group, respectively. The biochemical and microorganism indices also indicated that the E-group treatment yielded better results on thawing than the R-group treatment. The application of this model has the potential to keep products fresh.

Relative hypoparathyroidism (parathyroid hormone [PTH] < or = 200 pg/mL) is prevalent in hemodialysis (HD) patients, with unknown pathogenesis and prognosis. Thus, to clarify risk factors and prognosis of time-dependent relative hypoparathyroidism in HD patients, a retrospective cohort study was performed for 126 HD patients with four or more PTH determinations and no previous total or subtotal parathyroidectomy. Values for intact PTH, ionized calcium, phosphate, magnesium, albumin, creatinine, urea reduction ratio (URR), glucose, hemoglobin A1c (HbA1c), aluminum, and 1,25(OH)2D were obtained at enrollment and at some time during follow-up. The prevalence of relative hypoparathyroidism at entry was 76 of 126 patients (60.3%). Univariate analysis showed that patients with hypoparathyroidism were older, more likely to have diabetes, and had greater ionized calcium levels and lower phosphate, albumin, blood urea nitrogen (BUN), and creatinine levels. Patients with diabetes were older and had a shorter duration of dialysis therapy and lower PTH, phosphate, albumin, BUN, and creatinine levels and URRs. Conversely, multivariate analysis showed that PTH levels at entry were associated directly with creatinine levels and inversely with age and ionized calcium levels (but not diabetes). During follow-up, PTH levels fluctuated concomitantly with ionized calcium and phosphate levels over time in all patients. Time-dependent PTH levels were associated directly with duration of dialysis therapy and use of vitamin D and phosphate and albumin levels, but inversely with age and ionized calcium and magnesium levels (but not glucose or HbA1c levels). Interestingly, time-dependent PTH levels were independently associated with survival after adjusting for traditional risk factors (diabetes, age, albumin and creatinine levels, and URR) and duration of dialysis therapy. We conclude that in HD patients, relative hypoparathyroidism was not associated with diabetes per se. Time-dependent PTH levels were associated with age, duration of dialysis, and levels of ionized calcium, phosphate, albumin, and magnesium. Moreover, relative hypoparathyroidism at entry and lower time-dependent PTH levels predict mortality.