Feature-weight based measurement of cancerous transcriptome using cohort-wide and sample-specific information.

Identifying cancerous samples or cells using transcriptomic data is critical for cancer related basic research, early diagnosis, and targeted therapy. However, the high transcriptional heterogeneity of cancers still hinders people from accurately recognizing cancerous transcriptome using bulk, single-cell, or spatial RNA-seq data. Here, we present a novel method named FWP (Feature Weight Pro) that helps measure cancerous transcriptome using transcriptomic data. The workflow of FWP is, first, to calculate feature weights using the training dataset, and then, for each sample in the testing dataset, calculate the feature-weight based final score by combining the cohort-wide and sample-specific information. Those two types of information are utilized through conducting weighted principal component analysis and calculating correlation perturbations. The effectiveness and superiority of FWP over other methods are shown by using bulk, single-cell, and spatial RNA-seq data of multiple cancer types. In addition, the high robustness and efficiency of FWP are also demonstrated by using different numbers of features and cells, respectively. FWP is available at https://github.com/jumphone/fwp .

Mode-tunable, micro/nanoscale electrohydrodynamic deposition techniques for optoelectronic device fabrication.

The rapid development of fascinating new optoelectronic materials and devices calls for the innovative production of micro/nanostructures in a high-resolution, large-scale, low-cost fashion, preferably compatible with flexible/wearable applications. Powerful electrohydrodynamic (EHD) deposition techniques, which generate micro/nanostructures using high electrical forces, exhibit unique advantages in high printing resolution (<1 µm), tunable printing modes (electrospray for films, electrospinning for fibers and EHD jet printing for dots), and wide material applicability (viscosity 1-10 000 cps), making them attractive in the fabrication of high-density and high-tech optoelectronic devices. This review highlights recent advances related to EHD-deposited optoelectronics, ranging from solar cells, photodetectors, and light-emitting diodes, to transparent electrodes, with detailed descriptions of the EHD-based jetting mechanism, ink formulation requirements and corresponding jetting modes to obtain functional micro/nanostructures. Finally, a brief summary and an outlook on the future perspectives are proposed.

A MCL-1-targeted photosensitizer to combat triple-negative breast cancer with enhanced photodynamic efficacy, sensitization to ROS-induced damage, and immune response.

As growth factor receptor-2 (HER-2), progesterone receptor (PR) and estrogen receptor (ER) are scarce in triple-negative breast cancer (TNBC), it is a great challenge to combat TNBC with high tumor specificity and therapeutic efficacy. Most traditional treatments including surgical resection, chemotherapy, and radiotherapy would more or less cause serious side effects and drug resistance. Photodynamic therapy (PDT) has huge potential in the treatment of TNBC for minimal invasiveness, low toxicity, less drug resistance and high spatiotemporal selectivity. Inspired by the advantages of small-molecule-targeted PDT and the sensitization effect of myeloid cell leukemia-1 (MCL-1) inhibitor, a novel photosensitizer BC-Pc was designed by conjugating MCL-1 inhibitor with zinc phthalocyanines. Owning to 3-chloro-6-methyl-1-benzothiophene-2-carboxylic acid (BC) moiety, BC-Pc exhibits the high affinity towards MCL-1 and reduce its self-aggregation in TNBC cells. Therefore, MCL-1 targeted BC-Pc showed remarkable intracellular fluorescence and ROS generation in TNBC cells. Additionally, BC-Pc can selectively sensitize TNBC cells to ROS-induced damage, resulting in improved therapeutic effect to TNBC cells and negligible toxicity to normal cells. More importantly, BC-Pc can effectively inhibit the migration and invasion of TNBC cells, and enhance immune response, all of which will be beneficial to eradicate TNBC. To the best of our knowledge, BC-Pc is the novel MCL-targeted photosensitizer, which owns the amplified ROS-induced lethality and anticancer immune response for TNBC. Overall, our study provides a promising strategy to achieve targeting and highly efficient therapy of TNBC.

A Chromosome-Level Genome Assembly of the Pygmy Mole Cricket Xya riparia.

The pygmy mole cricket Xya riparia (Orthoptera: Tridactyloidea) is rarely studied or widely known. Some species of pygmy mole crickets, however, not only have a potential ecological value but are also important in the study of the evolution of the orthopteran genome and its phylogenetic relationships. The genome resources of pygmy crickets are limited and there are currently no publications referencing this species' genome. In this study, we assembled a reference genome of X. riparia at the chromosomal level using nanopore sequencing and Hi-C technology. An X. riparia genome of 1.67 Gb was successfully assembled from 164.01 Gb of nanopore sequencing data. The genome assembly showed a completeness of 98.97% benchmarking universal single-copy orthologs with a contig N50 of 4.18 Mb and the longest contig being 18.84 Mb. The contigs were clustered, ordered, and correctly oriented on six pseuchromosomes, which covered 95.63% of the genome assembly through Hi-C data with a scaffold N50 of 319.1 Mb and the longest scaffold being 397.8 Mb. Repeat sequences accounted for 42.88% of the whole-genome assembly. A total of 60,847 noncoding RNAs were detected. Moreover, 16,468 (87.91%) of the genes were functionally annotated. As this is the first high-quality reference genome of X. riparia at the chromosomal level, it will undoubtedly serve as a valuable resource for ecological, biological, and genetic research on pygmy mole crickets as well as for general research on Orthoptera's genome evolution and phylogenetic relationships.

Spectroscopic characterization of dissolved organic matter from macroalgae Ulva pertusa decomposition and its binding behaviors with Cu(II).

Dissolved organic matter (DOM) from macroalgae is regarded a crucial source of autochthonous DOM in coastal ocean. In the present study, the characteristics of DOM from the macroalgae Ulva pertusa decomposition (U. pertusa-DOM) and its binding behaviors with Cu(II) using multiple spectroscopic techniques and chemometric analyses. The labile U. pertusa-DOM could be consumed and transformed by microorganisms. The absorption spectroscopic descriptors indicate that the hydrophobicity, aromaticity, and molecular weight of the U. pertusa-DOM increase during the 27-day incubation period. Fluorescence excitation-emission matrix spectroscopy combined with parallel factor analysis suggests that the relative abundance of the protein-like component (C1) (96.10-84.96%) sequentially decreases, whereas the humic-like components (C2) (2.16-9.73%) and (C3) (1.75-5.31%) in the U. pertusa-DOM increase with the U. pertusa decomposition. The Cu(II) binding properties of the U. pertusa-DOM are dependent on the decomposition time. The order of the conditional stability constant (logKM) is C2 > C1 > C3. The complexation capacity (f) of C1 is higher than those of C2 and C3 at a specific time. Synchronous fluorescence spectroscopy coupled with two-dimensional correlation spectroscopy reveals that the microbial degradation could accelerate the Cu(II) binding to humic-like fractions in the U. pertusa-DOM. These findings will help us better understand the biogeochemical behaviors of macroalgal DOM and heavy metal in coastal ecosystems.

[Clinical features of 89 patients with primary non-Hodgkin's lymphoma of the tonsil].

BACKGROUND & OBJECTIVE: Head and neck lymphoma develops predominantly in the tonsil. This study was to investigate the clinical features of primary non-Hodgkin's lymphoma (NHL) of the tonsil, and to explore possible ways to improve the prognosis and quality of life of the patients after treatment. METHODS: Clinical data of 89 naive patients with NHL of the tonsil, treated from May 1990 to Jan. 2003, were retrospectively reviewed. All patients were confirmed pathologically and classified according to revised European-American Lymphoid Neoplasms and World Health Organization Classification, and staged according to the Ann Arbor classification. Stage I-II patients received radiochemotherapy-predominant treatment, whereas stage III-IV patients received chemotherapy-predominant treatment. RESULTS: Of the 89 cases, 60 (67%) were diffuse large B-cell subtype, 11 (12%) were peripheral T-cell subtype, 5 (6%) were indolent lymphoma, 1 was anaplastic large T-cell lymphoma, and 1 was T lymphoblastic lymphoma; 81 (91%) were stage I-II disease. Of the 89 patients, 58 (72%) received radiochemotherapy, 19 (21%) received radiotherapy alone, 3 received chemotherapy alone, and 1 received radiochemotherapy combined with rituximab. The 5-year overall survival rate was 80%, that of stage I-II patients was 84%. Cox regression multivariate analysis showed that the survival rate was correlated to the value of international prognostic index (IPI), and whether the patient had primary refractory or relapsed disease, but was not correlated to sex, age, pathologic subtype, B symptoms, and bulky disease. CONCLUSIONS: Most patients with NHL of the tonsil are at early stages, with good prognosis. Diffuse large B-cell lymphoma is the most common pathologic subtype. Primary refractory, relapse, and IPI>1 are independent prognostic factors.

[Clinical analysis of 68 patients with primary gastric lymphoma].

BACKGROUND & OBJECTIVES: Stomach is the most common extranodal involvement site of lymphoma. Treatment patterns for primary gastric lymphoma (PGL) are controversial now. This study was to investigate clinical features, treatment patterns, and prognostic factors of patients with PGL. METHODS: Records of 68 patients with PGL, including 37(54.4%) men,and 31(45.6%) women with a median age of 50(25-82) years,were retrospectively analyzed. Thirty-seven patients received surgery plus chemotherapy,7 received surgery plus chemoradiotherapy,9 received surgery plus radiotherapy,9 received surgery plus chemotherapy, 4 received surgery alone,and 2 were untreated. Survival rate was calculated by Kaplan-Meier method,prognosis factors were analyzed by univariate analysis, and Cox model multivariate analysis. RESULTS: Common symptoms of PGL were abdominal pain, and weight loss. Common lesions of PGL were in gastric body, and gastric antrum. All 68 patients with PGL were diagnosed of non-Hodgkin's lymphoma (NHL) by pathology, which constituted about 3.4% of all gastric malignancies synchronously, 1 was T cell original, 67 were B cell original. Diagnosis rate of gastroscopy biopsy was 53.2%, that of X-ray barium meal was 40.9%. The overall 1-, 3-, and 5-year survival rates were 90.5%, 78.2%, and 75.7%, respectively. Univariate analysis showed that clinical stage (Ann Arbor), international prognostic index (IPI), and surgery were significant prognostic factors for PGL patients. Cox model multivariate analysis indicated that only surgery was independent prognostic factor for PGL patients. CONCLUSIONS: Treatment of PGL should be based on combined therapy of surgery, chemotherapy, and radiotherapy. Surgery may be an independent prognostic factor for PGL patients.

[Primary central nervous system lymphoma: a report of 28 patients].

OBJECTIVE: To evaluate the clinical characteristics, reasonable mode of treatment and prognostic factors in patients with primary central nervous system lymphoma (PCNSL). METHODS: Twenty-eight patients with PCNSL treated from 1989 to 2002 were retrospectively reviewed. The clinical characteristics, results of treatment and prognostic factors were analyzed by SPSS10.0 statistic software. RESULTS: Of 28 patients, 18 men and 10 women with a median age of 52 years. The median survival time was 2 years (range 6 months-6 years). The 5-year survival rate was 21.4%. Nineteen patients had single-locus lesion and 9 multi-locus lesion, 78.6% of the patients were diagnosed as having B-cell origin, its main type being diffuse large cell lymphoma. According to international working formulation (WF), moderate-grade of histopathology was observed in 57.7% (15/28). Cox regression analysis revealed that single- or multi-locus lesion was only independent prognostic factor (P = 0.0417). Combined chemotherapy showed significant efficacy for those patients who had lesion of B-cell origin, high grade or multi-locus lesion, and the efficacy of irregular chemotherapy was better than that of regular chemotherapy. CONCLUSION: Primary central nervous system lymphoma has a special prognostic factor. Chemotherapy plays a very important role in comprehensive treatment, irregular chemotherapy should be adopted as a regular treatment.

[Primary non-Hodgkin lymphoma in the female genital system: a report of 28 cases].

OBJECTIVE: To evaluate the clinical characteristics, results of treatment, and prognostic factors of patients diagnosed as having primary female genital system lymphoma (PFGSL). METHODS: Twenty-eight cases of PFGSL were retrospectively surveyed and the clinical data of the patients were analyzed by statistic software package of SPSS10.0 for relation between clinical stage, grade, pathologic feature, treatment and prognosis. RESULTS: The median age was 44 in the cohort. It mainly involved cervix uterus, ovary and vulva. The disease had a broad range of pathologic type and 20 patients were diagnosed as suffering from B-cell by immunophenotyping, 4 patients were diagnosed as T-cell and 4 patients lesions were indefinite. According to International Working Formulation (IWF), 66.7% belonged to the intermediate-grade. The Ann Arbor stage included: Stage I(E)-12 pts (42.86%), Stage II(E)-3 pts (10.7%), Stage III(E)-1 pts (3.6%) and Stage IV-12 pts (42.86%). According to International Prognostic Index (IPI), 10 were low risk, 9 low-medium risk, 3 medium-high risk and 6 high risk, The median follow-up of the surviving patients was 2.0 years (range: 3 months-17 years), The 5-year overall survival rate was 39.3%. Most patients were given comprehensive treatment without any mode showing significant advantage over the others in survival (P = 0.2554), The involved organs, Ann Arbor stage, IWF and also IPI were significant prognostic factors for survival, CONCLUSION: The management of PFGSL should be based on comprehensive treatment including chemotherapy as the chief means. The significant prognostic factors of survival is Ann Arbor stage, IPI, IWF and the kind of involved organs.