Constrained Online Two-stage Stochastic Optimization: Algorithm with (and without) Predictions

We consider an online two-stage stochastic optimization with long-term constraints over a finite horizon of $T$ periods. At each period, we take the first-stage action, observe a model parameter realization and then take the second-stage action from a feasible set that depends both on the first-stage decision and the model parameter. We aim to minimize the cumulative objective value while guaranteeing that the long-term average second-stage decision belongs to a set. We develop online algorithms for the online two-stage problem from adversarial learning algorithms. Also, the regret bound of our algorithm can be reduced to the regret bound of embedded adversarial learning algorithms. Based on this framework, we obtain new results under various settings. When the model parameters are drawn from unknown non-stationary distributions and we are given machine-learned predictions of the distributions, we develop a new algorithm from our framework with a regret $O(W_T+\sqrt{T})$, where $W_T$ measures the total inaccuracy of the machine-learned predictions. We then develop another algorithm that works when no machine-learned predictions are given and show the performances.Comment: arXiv admin note: substantial text overlap with arXiv:2302.0099

Recognition of protein/gene names from text using an ensemble of classifiers

This paper proposes an ensemble of classifiers for biomedical name recognition in which three classifiers, one Support Vector Machine and two discriminative Hidden Markov Models, are combined effectively using a simple majority voting strategy. In addition, we incorporate three post-processing modules, including an abbreviation resolution module, a protein/gene name refinement module and a simple dictionary matching module, into the system to further improve the performance. Evaluation shows that our system achieves the best performance from among 10 systems with a balanced F-measure of 82.58 on the closed evaluation of the BioCreative protein/gene name recognitiontask (Task 1A)

Relationships Between Key Dryland Ecosystem Services: A Case Study in Ordos, China

Dryland ecosystem services (ESs) have been severely harmed by global environmental changes and increased human activities. To improve ESs, it is necessary to understand how they interact in drylands. In this study, we selected Ordos dryland, which is situated in northern China, as the study area to assess its four key ESs—food supply (FS), carbon storage (CS), water yield (WY), and habitat quality (HQ)—and to identify the hotspots of multiple ES supply. Furthermore, we studied the constraint effects between ESs in Ordos in 2000, 2010, and 2020 and used a spatial trade-off model to map the trade-off and synergy areas of ESs from 2000 to 2010 and from 2010 to 2020. The results indicated that all four ESs in Ordos increased significantly over the study period. The hotspots for the supply of multiple ESs also increased in areal extent during this period, and the state of the regional ecological environment continued to improve. The constraint effect between ESs showed that as the CS increased, its constraint effect on WY and FS decreased and then increased, whereas its constraint effect on HQ only decreased; as the WY increased, its constraint effect on HQ decreased and then increased, and its constraint effect on FS continued to decrease; as the FS increased, its constraint effect on HQ continued to increase. From the change in the area of ESs trade-offs and synergies, there was an increase in the area of positive synergy for four pairs of ESs in Ordos, which were CS-WY, CS-HQ, WY-HQ, and FS-HQ. These findings help in establishing a scientific foundation for the management and optimization of ESs in drylands

Skewed X-chromosome inactivation in patients with esophageal carcinoma

ABSTRACT: Skewed X-chromosome inactivation (SXCI) was found in some apparently healthy females mainly from Western countries. It has been linked to development of ovarian, breast and pulmonary carcinomas. The present study aimed to observe the SXCI frequencies in apparently healthy Chinese females and patients with esophageal carcinoma. DNA was extracted from the peripheral blood cells from 401 Chinese females without a detectable tumor and 143 female patients with esophageal carcinoma. Exon 1 of androgen receptor (AR) gene was amplified, and the products of different CAG alleles were resolved on denaturing polyacrylamide gels and visualized after silver staining. The corrected ratios (CR) of the products before and after HpaII digestion were calculated. As to the healthy females, when CR ≥ 3 was used as a criterion, SXCI was found in two (4.3%) of the 46 neonates, 13 (7.8%) of the 166 younger adults (16–50 years) and 37 (25.7%) of the 144 elderly females (51–96 years), with the frequency higher in the elderly subjects than in the two former groups (P < 0.05). When a more stringent criterion (CR ≥ 10) was used, SXCI was found in one (2.2%), two (1.2%) and 16 (11.1%) of the subjects in the three age groups, respectively, itsfrequency being higher in the elderly than in the younger age groups (P < 0.05). Occurrence of SXCI was detected in both the patients and controls at similar frequencies. However, the phenomenon, as defined as CR ≥ 3, was more frequent in the patients aging <40 years (35.7%) compared to the corresponding reference group (7.6%, P = 0.006). When CR ≥ 10 was adopted, the frequencies were 7.1% and 1.2%, respectively. Their difference did not attain statistical significance (P = 0. 217). SXCI also occurs in apparently healthy Chinese females, and is associated with age. It may be considered as a predisposing factor for the early development of esophageal carcinoma. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here http://www.diagnosticpathology.diagnomx.eu/vs/154236433792765

High-strong-ductile magnesium alloys by interactions of nanoscale quasi-long period stacking order unit with twin.

Magnesium alloys with high strength in combination of good ductility are especially desirable for applications in transportation, aerospace and bio-implants owing to their high stiffness, abundant raw materials, and environmental friendliness. However, the majority of traditional strengthening approaches including grain refining and precipitate strengthening can usually prohibit dislocation movement at the expense of ductility invariably. Herein, we report an effective strategy for simultaneously enhancing yield strength (205 MPa, 2.41 times) and elongation (23%, 1.54 times) in a Mg-0.2Zn-0.6Y (at.%) alloy at room temperature, based on the formation of a nanosized quasi-long period stacking order unit (QLPSO)-twin structure by ultrahigh-pressure treatment followed by annealing. The formation reason and strong-ductile mechanism of the unique QLPSO-twin structure have been clarified by transmission electron microscopy observations and molecule dynamics simulations. The improved strength is mainly associated with the presence of nanosized QLPSO and the modified <86.3o QLPSO-twin boundary (TB) interface, effectively pinning dislocation movement. Comparatively, the enhanced ductility is related to the <3.7o QLPSO-TB interface and micro-kinks of nanoscale QLPSO, providing some paths for plastic deformation. This strategy on the QLPSO-twin structure might provide an alternative perspective for designing innovative hexagonal close-packed structural materials with superior mechanical properties

ChemDFM: Dialogue Foundation Model for Chemistry

Large language models (LLMs) have established great success in the general domain of natural language processing. Their emerging task generalization and free-form dialogue capabilities can greatly help to design Chemical General Intelligence (CGI) to assist real-world research in chemistry. However, the existence of specialized language and knowledge in the field of chemistry, such as the highly informative SMILES notation, hinders the performance of general-domain LLMs in chemistry. To this end, we develop ChemDFM, the first LLM towards CGI. ChemDFM-13B is trained on 34B tokens from chemical literature, textbooks, and instructions as well as various data from the general domain. Therefore, it can store, understand, and reason over chemical knowledge and languages while still possessing advanced free-form language comprehension capabilities. Extensive quantitative evaluation shows that ChemDFM can significantly outperform the representative open-sourced LLMs. Moreover, ChemDFM can also surpass GPT-4 on a great portion of chemical tasks, despite the significant size difference. Further qualitative evaluations demonstrate the efficiency and effectiveness of ChemDFM in real-world research scenarios. We will open-source the ChemDFM model soon.Comment: 10 pages, 12 figures, 13 tables. Under Revie

Downregulated miR-195 Detected in Preeclamptic Placenta Affects Trophoblast Cell Invasion via Modulating ActRIIA Expression

Preeclampsia (PE) is a pregnancy-specific syndrome manifested by on-set of hypertension and proteinuria after 20 weeks of gestation. Abnormal placenta development has been generally accepted as initial cause of the disorder. Recently, miR-195 was found to be down-regulated in preeclamptic placentas compared with normal pregnant ones, indicating possible association of this small molecule with placental pathology of preeclampsia. By far the function of miR-195 in the development of placenta remains unknown.Bioinformatic assay predicted ActRIIA as one of the targets for miR-195. By using Real-time PCR, Western blotting and Dual Luciferase Assay, we validated that ActRIIA was the direct target of miR-195 in human trophoblast cells. Transwell insert invasion assay showed that miR-195 could promote cell invasion in trophoblast cell line, HTR8/SVneo cells, and the effect could be abrogated by overexpressed ActRIIA. In preeclamptic placenta tissues, pri-miR-195 and mature miR-195 expressions were down-regulated, whereas ActRIIA level appeared to be increased when compared with that in gestational-week-matched normal placentas.This is the first report on the function of miR-195 in human placental trophoblast cells which reveals an invasion-promoting effect of the small RNA via repressing ActRIIA. Aberrant expression of miR-195 may contribute to the occurrence of preeclampsia through interfering with Activin/Nodal signaling mediated by ActRIIA in human placenta

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

<p>Abstract</p> <p>Background</p> <p>The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.</p> <p>Results</p> <p>One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (<it>p </it>≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including <it>WNT10B </it>and <it>DKK2 </it>in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- <it>BAX </it>and <it>BMPR1B </it>were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (<it>p </it>≤ 0.1 or <it>p </it>≤ 0.05).</p> <p>Conclusions</p> <p>Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of <it>BAX </it>and <it>BMPR1B </it>gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.</p

Isolates of Liao Ning Virus from Wild-Caught Mosquitoes in the Xinjiang Province of China in 2005

Liao ning virus (LNV) is related to Banna virus, a known human-pathogen present in south-east Asia. Both viruses belong to the genus Seadornavirus, family Reoviridae. LNV causes lethal haemorrhage in experimentally infected mice. Twenty seven isolates of LNV were made from mosquitoes collected in different locations within the Xinjiang province of north-western China during 2005. These mosquitoes were caught in the accommodation of human patients with febrile manifestations, or in animal barns where sheep represent the main livestock species. The regions where LNV was isolated are affected by seasonal encephalitis, but are free of Japanese encephalitis (JE). Genome segment 10 (Seg-10) (encoding cell-attachment and serotype-determining protein VP10) and Seg-12 (encoding non-structural protein VP12) were sequenced for multiple LNV isolates. Phylogenetic analyses showed a less homogenous Seg-10 gene pool, as compared to segment 12. However, all of these isolates appear to belong to LNV type-1. These data suggest a relatively recent introduction of LNV into Xinjiang province, with substitution rates for LNV Seg-10 and Seg-12, respectively, of 2.29×10−4 and 1.57×10−4 substitutions/nt/year. These substitution rates are similar to those estimated for other dsRNA viruses. Our data indicate that the history of LNV is characterized by a lack of demographic fluctuations. However, a decline in the LNV population in the late 1980s - early 1990s, was indicated by data for both Seg-10 and Seg-12. Data also suggest a beginning of an expansion in the late 1990s as inferred from Seg-12 skyline plot