HervD Atlas: a curated knowledgebase of associations between human endogenous retroviruses and diseases

Human endogenous retroviruses (HERVs), as remnants of ancient exogenous retrovirus infected and integrated into germ cells, comprise ∼8% of the human genome. These HERVs have been implicated in numerous diseases, and extensive research has been conducted to uncover their specific roles. Despite these efforts, a comprehensive source of HERV-disease association still needs to be added. To address this gap, we introduce the HervD Atlas (https://ngdc.cncb.ac.cn/hervd/), an integrated knowledgebase of HERV-disease associations manually curated from all related published literature. In the current version, HervD Atlas collects 60 726 HERV-disease associations from 254 publications (out of 4692 screened literature), covering 21 790 HERVs (21 049 HERV-Terms and 741 HERV-Elements) belonging to six types, 149 diseases and 610 related/affected genes. Notably, an interactive knowledge graph that systematically integrates all the HERV-disease associations and corresponding affected genes into a comprehensive network provides a powerful tool to uncover and deduce the complex interplay between HERVs and diseases. The HervD Atlas also features a user-friendly web interface that allows efficient browsing, searching, and downloading of all association information, research metadata, and annotation information. Overall, the HervD Atlas is an essential resource for comprehensive, up-to-date knowledge on HERV-disease research, potentially facilitating the development of novel HERV-associated diagnostic and therapeutic strategies.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.

Clinical Value of Hybrid TOF-PET/MR Imaging-Based Multiparametric Imaging in Localizing Seizure Focus in Patients with MRI-Negative Temporal Lobe Epilepsy

BACKGROUND AND PURPOSE

Temporal lobe epilepsy is the most common type of epilepsy. Early surgical treatment is superior to prolonged medical therapy in refractory temporal lobe epilepsy. Successful surgical operations depend on the correct localization of the epileptogenic zone. This study aimed to evaluate the clinical value of hybrid TOF-PET/MR imaging-based multiparametric imaging in localizing the epileptogenic zone in patients with MR imaging-negative for temporal lobe epilepsy.

MATERIALS AND METHODS

Twenty patients with MR imaging-negative temporal lobe epilepsy who underwent preoperative evaluation and 10 healthy controls were scanned using PET/MR imaging with simultaneous acquisition of PET and arterial spin-labeling. On the basis of the standardized uptake value and cerebral blood flow, receiver operating characteristic analysis and a logistic regression model were used to evaluate the predictive value for the localization. Statistical analyses were performed using statistical parametric mapping. The values of the standardized uptake value and cerebral blood flow, as well as the asymmetries of metabolism and perfusion, were compared between the 2 groups. Histopathologic findings were used as the criterion standard.

RESULTS

Complete concordance was noted in lateralization and localization among the PET, arterial spin-labeling, and histopathologic findings in 12/20 patients based on visual assessment. Concordance with histopathologic findings was also obtained for the remaining 8 patients based on the complementary PET and arterial spin-labeling information. Receiver operating characteristic analysis showed that the sensitivity and specificity of PET, arterial spin-labeling, and combined PET and arterial spin-labeling were 100% and 81.8%, 83.3% and 54.5%, and 100% and 90.9%, respectively. When we compared the metabolic abnormalities in patients with those in healthy controls, hypometabolism was detected in the middle temporal gyrus (P < .001). Metabolism and perfusion asymmetries were also located in the temporal lobe (P < .001).

CONCLUSIONS

PET/MR imaging-based multiparametric imaging involving arterial spin-labeling may increase the clinical value of localizing the epileptogenic zone by providing concordant and complementary information in patients with MR imaging-negative temporal lobe epilepsy.

[Clinical Application Value of Peripheral Blood Diagnostic Report]

Objective: To explore the clinical application value of peripheral blood diagnostic report. Methods: 557 peripheral blood diagnostic reports were collected from Peking University First Hospital, YANDA LU DAOPEI Hospital and Beijing United Family Hospital. The results were analyzed and summarized according to different blood cell morphology character for the first time and review cases, respectively. Results: Two hundred and one samples from first time patients were found abnormal complete blood count or leukocyte differential count, they were summarized as anemia, anemia accompanied with leukopenia or thrombopenia, abnormal white blood cell count or leukocyte differential count and abnormal platelet count. Each condition was further distinguished on the basis of different morphology character. Initial diagnosis or further examination could be proposed if abnormal morphology was specific or typical, when blood cell morphology was atypical or normal, the morphology was described objectively. 22 review cases included many benign and malignant disorders such as acute leukemia, chronic leukemia, myelodysplastic syndrome, multiple myeloma, infectious mononucleosis and so on. Suggestion of therapeutic effect, progression of diseases or further examination could be present according to complete blood cell count and morphology character. Conclusion: Peripheral blood diagnostic report can provide more comprehensive and accurate information for clinic, and propose important advisory opinions for primary diagnosis, differential diagnosis, treatment monitoring and progression assessment.

[Effects and its mechanism of Nimotuzumab on radiosensitivity of esophageal carcinoma ECA-109 and TE-13 cell lines]

Objective: To investigate the effects of nimotuzumab on radiosensitivity of ECA-109 and TE-13 esophageal carcinoma cell lines and explore its possible mechanism. Methods: The ECA-109 and TE-13 cells were divided into control group, irradiation group, medicine group, and combined group (irradiation + medicine). In the combined group, ECA-109 and TE-13 cells were treated with nimotuzumab for 24 h before irradiation, and the cells were collected 2 h after irradiation. The radiosensitizing effects of nimotuzumab on ECA-109 and TE-13 cells were evaluated by clone formation assay. Cell apoptosis was detected by flow cytometry. Western blotting was used to evaluate the expression of EGFR, p-EGFR, DNA-PKcs, p-DNA-PKcs and γH2AX. Results: The values of D_q (quasithreshold dose), D₀(mean lethal dose)and SF₂ (surviving fraction at 2 Gy) of ECA-109 and TE-13 cells in the combined group were significantly lower than those of the radiation group (for ECA-109 cells, 1.11 vs. 1.72, 1.40 vs. 2.14, 0.42 vs. 0.66, respectively; for TE-13 cells, 0.41 vs. 0.46, 0.43 vs. 0.65, 0.40 vs. 0.71, respectively (all P<0.05). The sensitivity enhancement ratio (SER) of ECA-109 and TE-13 cells were 1.35 and 1.43, respectively. Flow cytometry showed that the apoptosis rate of ECA-109 and TE-13 cells in the combined group were significantly higher than those of the radiation group [for ECA-109 cells, (41.31±1.52)% vs. (9.54±0.52)%; for TE-13 cells, (46.28±0.28)% vs. (11.32±0.31)%, both P<0.01]. Western blotting showed that the expression levels of EGFR and DNA-PKcs were not significantly different in all groups (all P>0.05). Compared with those of the control group, p-EGFR and p-DNA-PKcs of the radiation group were significantly higher in both cell lines (P<0.05), and the γH2AX levels in the radiation group and medicine group were significantly higher than that of the control group (P<0.05). Compared with those of the radiation group and medicine group, p-EGFR and p-DNA-PKcs protein expression in the combined group were decreased significantly (P<0.05), while γH2AX protein expression was significantly increased (P<0.05). Conclusions: Nimotuzumab can enhance the radiosensitivity of esophageal cancer ECA-109 and TE-13 cells. The potential mechanism may be related to the inhibition of EGFR phosphorylation and down-regulation of DNA damage repair proteins. The radiosensitizing effect of nimotuzumab is greater on poorly differentiated esophageal cancer cells.

[Clinical effects of Dynesys system and transfacet decompression through Wiltse approach in the treatment of lumbar degenerative diseases]

Objective: To investigate the early clinical effects of Dynesys system and transfacet decompression by Wiltse approach in the treatment of lumbar degenerative diseases. Methods: From January 2010 to December 2013, 48 patients suffering from lumbar degenerative diseases were treated with Dynesys system in addition to transfacet decompression through Wiltse approach.There were 28 males and 20 females with age of (51.8±6.8). The preoperative diagnosis included lumbar spinal stenosis(10 cases); lumber intervertebral disc herniation (38 cases). There were 23 cases in L4/5, 16 cases in L5/S1 and 9 cases in both of L4/5 and L5/S1.Posterolateral fixation with Dynesys pedicle screw through Wiltse approach.Unilateral resection of the inferior articular facet of the superior vertebra and the superior articular facet of the inferior vertebra.Decompression of the vertebral canal until the never root was decompressed satisfactorily.In the end, Dynesys was performed according to normal procedure.VAS, ODI evaluating standards were applied to evaluate the therapeutic effect.The intervertebral space and ROM of the lumbar were observed by X ray. Results: All patients underwent surgery safely without severe complications occurred.The average following up time was 33.5 (24-60) months.Compared with preoperative parameters (7.7±1.3, 70.8±13.5), the scores of VAS and ODI decreased significantly after surgery (2.3±1.5, 23.6±12.2) and at the final follow-up (2.2±1.4, 20.0±9.8) (P<0.05). There were significant difference in the height of intervertebral space and ROM at the stabilized segment (P<0.05), but no significant changes were seen at the adjacent segments (P>0.05). X-ray scan showed neither instability or internal fixation loosen, breakage or distortion in follow-up. Conclusion: Dynesys system in addition to transfacet decompression through Wiltse approach is a therapy option for mild lumbar degenerative disease.This method can retention the structure of lumbar posterior complex and the activity of the fixed segment, reduce the risk of low back pain together with nerve root decompressed.The early clinical results are satisfactory.

[Formation of mouse chimeras from early embryonic pluripotential stem cell]

Three chimeric mice were produced by injecting the embryonic stem cell-CCE cells into the cavity of 3.5 day host blastocysts from Kunming and C57BL/6J mice. By analyses of glucose phosphate isomerase (GPI-1), the results show a contribution from CCE cells in heart tissue of female Kunming chimera. Breeding experiments demonstrated that all chimeric mice were fertile but none of 3 chimeras produced germ line transmission.

[Enzyme-linked immunosorbent assay of larvicidal toxic proteins of Bacillus sphaericus Ts-1]

Bacillus sphaericus Ts-1 Mosquito larvicidal toxins 42 k Da and 43 k Da were isolated by Sephadex G-200 chromatography. Three strains of highly toxic B. sphaericus and two non toxic strains were screened for toxic proteins using ELISA. The lowest detectable toxin level was 1.56 X 10(-5) mg/ml. Non toxic strains did not produce antigens reacting to either the 42 kDa or the 43 kDa antibodies. Ts-1 cultures were examined at 12 and 24 h by LC50 bioassay against Culex pipiens. The LC50's at 12 h and 24 h were 0.71 ppm and 0.154 ppm, respectively, i.e., the toxin level at 24 h was 4.6 times the level at 12 h. ELISA tests established total toxin at 0.049 mg/ml and 0.225 mg/ml at 12 h and 24 h, respectively, confirming the LC50 study.

[Separation and purification of the toxic protein of Bacillus sphaericus Ts-1]

Bacillus sphaericus strain Ts-1 is highly insecticidal to larvae of the mosquito. It's insecticidal component is toxic proteins. The toxin was extracted from spore-crystal complexes by disruption in a Sonicator Cell Disruptor Model W-220F followed by treatment with 0.05 mol/L NaOH. Fraction recovered from chromatography of the spore-crystal complexes on column of Sephadex G-200 were assayed against mosquito larvae and the toxic fractions from gel chromatography were subjected to SDS-PAGE. The toxic proteins in B. sphaericus Ts-1 spore-crystal complex migrated in position corresponding to 42kD and 43kD. Bioassay of the two purified proteins prepared by PAGE indicated that they were all toxic to mosquito larvae. Toxic protein was further purified by DEAE-cellulose chromatography. The toxic protein with a molecular weight of 42kD was obtained.

Calmodulin regulation of the cholinergic receptor in the rat heart during ontogeny and senescence

The contents of calmodulin and cholinergic muscarinic receptor binding sites in the hearts of fetal, adult and aged rats have been examined. A biphasic pattern of calmodulin development was observed. A relatively high level of calmodulin appeared on gestational days 14-15 followed by a steady but significant decrease at birth and during the first week of postnatal life. The level of calmodulin then increased significantly during the first month followed by a decrease at 6 and 26 months of age. Calmodulin contents were significantly higher in the atrium than in the ventricle in the age groups of 1-26 months. The number of [3H]QNB binding sites showed a steady increase during the gestational periods studied, reaching a peak at 9 days after birth and followed by a significant (P less than 0.05) decline at 6 and 26 months of age. A good correlation between the levels of [3H]QNB binding and calmodulin was observed from day 9 of the postnatal period to 26 months of age. In the presence of calcium, calmodulin induced a dose-dependent receptor binding loss in the hearts of postnatal, young adult and aged rats under phosphorylating conditions. These findings support the suggestion that calmodulin may regulate cholinergic functions during ontogeny and senescence.