Signaling Transduction Network Mediated by Tumor Suppressor/Susceptibility Genes in NPC

Nasopharyngeal carcinoma (NPC) is a polygenetic disease. SPLUNC1, UBAP1, BRD7, NAG7, NOR1, NGX6 and LTF genes were found to be tumor suppressor/susceptibility genes in different stages of NPC. SPLUNC1, an early warning molecular diagnosis marker, inhibits the bacteria clone formation, and is an innated immune molecule. SPLUNC1 can negatively regulate the ERK/MAPK signaling transduction pathway to inhibit NPC cell proliferation and induce apoptosis. BRD7, a transcript regulation factor, interacts with BRD2, and promotes apoptosis induced by BRD2. Its promoter is regulated by c-Myc and SP1. BRD7 inhibits NPC cell cycle progression, preventing passage through G0/G1 by suppressing ras/MEK/ERK, Rb/E2F and Wnt signaling pathways. Abnormal activation of BRD7 is crucial to cell cycle turbulence in NPC. NGX6, a metastasis-associated protein, can negative-regulate the EGF/Ras/MAPK signaling transduction pathway, and interacts with ezrin protein to inhibit NPC cell invasion and metastasis. LTF, also a metastasis-associated protein, can negatively regulate MAPK signal transduction pathways, such as JNK2 and ERK, to inhibit NPC cell proliferation and growth. Taken together, it was found that these tumor suppressor/susceptibility genes can regulate key molecules involved in cell signal pathways such as ras/MEK/ERK, Rb/E2F and EGFR ras/MEK/MAPK, and can regulate the expression of some adhesion molecules such as ezrin, nm23 and α-catenin. According to functional genomics and signaling transduction pathways, we have described a signaling cross-talk network between the tumor suppressor/susceptibility genes involved in NPC. These tumor suppressor/susceptibility genes may be potential treatment targets for NPC in the future

Enhancing Throughput of Hadoop Distributed File System for Interaction-Intensive Tasks

Abstract-The performance of the Hadoop Distributed File System (HDFS)decreases dramatically when handling interactionintensive files, i.e., files that have relatively small size but are accessed frequently. The paper analyzes the cause of throughput degradation issue when accessing interaction-intensive files and presents an enhanced HDFS architecture along with an associated storage allocation algorithm that overcomes the performance degradation problem. Experiments have shown that with the proposed architecture together with the associated storage allocation algorithm, the HDFS throughput for interaction-intensive files increase 300% in average with only a negligible performance decrease for large data set tasks

Application of atomic force microscopy in cancer research

Atomic force microscopy (AFM) allows for nanometer-scale investigation of cells and molecules. Recent advances have enabled its application in cancer research and diagnosis. The physicochemical properties of live cells undergo changes when their physiological conditions are altered. These physicochemical properties can therefore reflect complex physiological processes occurring in cells. When cells are in the process of carcinogenesis and stimulated by external stimuli, their morphology, elasticity, and adhesion properties may change. AFM can perform surface imaging and ultrastructural observation of live cells with atomic resolution under near-physiological conditions, collecting force spectroscopy information which allows for the study of the mechanical properties of cells. For this reason, AFM has potential to be used as a tool for high resolution research into the ultrastructure and mechanical properties of tumor cells. This review describes the working principle, working mode, and technical points of atomic force microscopy, and reviews the applications and prospects of atomic force microscopy in cancer research

Fast Nearest Neighbor Machine Translation

Though nearest neighbor Machine Translation ($k$NN-MT) \citep{khandelwal2020nearest} has proved to introduce significant performance boosts over standard neural MT systems, it is prohibitively slow since it uses the entire reference corpus as the datastore for the nearest neighbor search. This means each step for each beam in the beam search has to search over the entire reference corpus. $k$NN-MT is thus two-orders slower than vanilla MT models, making it hard to be applied to real-world applications, especially online services. In this work, we propose Fast $k$NN-MT to address this issue. Fast $k$NN-MT constructs a significantly smaller datastore for the nearest neighbor search: for each word in a source sentence, Fast $k$NN-MT first selects its nearest token-level neighbors, which is limited to tokens that are the same as the query token. Then at each decoding step, in contrast to using the entire corpus as the datastore, the search space is limited to target tokens corresponding to the previously selected reference source tokens. This strategy avoids search through the whole datastore for nearest neighbors and drastically improves decoding efficiency. Without loss of performance, Fast $k$NN-MT is two-orders faster than $k$NN-MT, and is only two times slower than the standard NMT model. Fast $k$NN-MT enables the practical use of $k$NN-MT systems in real-world MT applications. The code is available at \url{https://github.com/ShannonAI/fast-knn-nmt}Comment: To appear at ACL 2022 Finding

Association between Virulence Factors and TRAF1/4-1BB/Bcl-xL

Objective. CagA+/vacAs1+/vacAm1+ Helicobacter pylori upregulates the expression of tumor necrosis factor receptor–associated factor 1 (TRAF1), tumor necrosis factor receptor superfamily member 9 (4-1BB), and B-cell lymphoma-extra large (Bcl-xL) in human gastric epithelial cells. We investigated the correlation between cagA/vacAs1/vacAm1 and TRAF1/4-1BB/Bcl-xL expression in gastric mucosal tissue of patients with gastric disorders. Methods. We collected gastric mucosa samples from 35 chronic, nonatrophic gastritis (CG) patients, 41 atrophic gastritis patients, 44 intestinal metaplasia with atypical hyperplasia (IM) patients, and 28 gastric carcinoma (Ca) patients. The expression of  TRAF1, 4-1BB, and Bcl-xL was determined using western blotting. The expression of cagA, vacAs1, and vacAm1 in H. pylori was examined with polymerase chain reaction. Results. The expression of TRAF1, 4-1BB, and Bcl-xL was significantly upregulated in IM and Ca patients (P<0.05 compared with CG). There were more cases of cagA+/vacAs1+/vacAm1+ H. pylori infection in samples with elevated TRAF1, 4-1BB, or Bcl-xL expression (P<0.05). Additionally, there were a remarkably large number of samples with upregulated TRAF1/4-1BB/Bcl-xL expression in cases of cagA+/vacAs1+/vacAm1+ H. pylori infection (44 cases, 67.7%; P<0.05). Conclusions. The pathogenesis of IM and Ca may be promoted by cagA+/vacAs1+/vacAm1+ H. pylori, possibly via upregulated TRAF1, 4-1BB, and Bcl-xL in gastric mucosal tissue

Isolation and Characterization of Microsatellite Loci in Pistacia weinmannifolia (Anacardiaceae)

Fourteen polymorphic microsatellite loci were isolated from the genomic DNA of Pistacia weinmannifolia, using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) method, and screened on 12 individuals from each of two wild populations. The 14 polymorphic loci had an average of 4.1 alleles per locus varying from 1 to 9. The observed (Ho) and expected (He) heterozygosities across the two populations ranged from 0.000 to 0.933 and from 0.000 to 0.906, respectively. Tests for departure from Hardy-Weinberg equilibrium (HWE) and genotypic linkage disequilibrium (LD) were conducted for each of the two populations separately. It was found that no locus significantly deviated from HWE proportions and no significant LD was detected between loci (p < 0.001). In the test of cross-species utility, we successfully amplified nine (64.2%) of 14 loci in P. chinensis and four (28.6%) in P. mexicana. The relatively high level of polymorphism for these markers will facilitate further studies of gene flow, population structure and evolutionary history of P. weinmannifolia and its congeners

Modeling the mid-piacenzian warm climate using the water isotope-enabled Community Earth System Model (iCESM1.2-ITPCAS)

The mid-Piacenzian Warm Period (MPWP, ~ 3.264–3.025 Ma) is the most recent example of a persistently warmer climate in equilibrium with atmospheric CO2 concentrations similar to today. Towards studying patterns and dynamics of a warming climate the MPWP is often compared to today. Following the Pliocene Model Intercomparison Project, Phase 2 (PlioMIP2) protocol we prepare a water isotope-enabled Community Earth System Model (iCESM1.2) simulation that is warmer and wetter than the PlioMIP2 multi-model ensemble (MME). While our simulation resembles PlioMIP2 MME in many aspects we find added insights. (1) Considerable warmth at high latitudes exceeds previous simulations. Polar amplification (PA) is comparable to proxies, enabled by iCESM1.2’s high climate sensitivity and a distinct method of ocean initialization. (2) Major driver of warmth is the downward component of clear-sky surface long-wave radiation. (3) In iCESM1.2 modulated dominance of dynamic (δDY) processes causes different low-latitude (~ 30 S°–10°N) precipitation response than the PlioMIP2 MME, where thermodynamic processes (δTH) dominate. (4) Modulated local condensation leads to lower δ18O across tropical Indian Ocean and surrounding Asian-African-Australian monsoon regions. (5) We find contrasting changes in tropical atmospheric circulations (Hadley and Walker cells). Anomalous regional meridional (zonal) circulation, forced by changes in tropical-subtropical (tropical) diabatic processes, presents a more comprehensive perspective than explaining weakened and expanded Hadley circulation (strengthened and westward-shifted Walker circulation) via static stability. (6) Enhanced Atlantic meridional overturning circulation owes to a closed Bering Strait