Differential evolutionary conservation of motif modes in the yeast protein interaction network

BACKGROUND: The importance of a network motif (a recurring interconnected pattern of special topology which is over-represented in a biological network) lies in its position in the hierarchy between the protein molecule and the module in a protein-protein interaction network. Until now, however, the methods available have greatly restricted the scope of research. While they have focused on the analysis in the resolution of a motif topology, they have not been able to distinguish particular motifs of the same topology in a protein-protein interaction network. RESULTS: We have been able to assign the molecular function annotations of Gene Ontology to each protein in the protein-protein interactions of Saccharomyces cerevisiae. For various motif topologies, we have developed an algorithm, enabling us to unveil one million "motif modes", each of which features a unique topological combination of molecular functions. To our surprise, the conservation ratio, i.e., the extent of the evolutionary constraints upon the motif modes of the same motif topology, varies significantly, clearly indicative of distinct differences in the evolutionary constraints upon motifs of the same motif topology. Equally important, for all motif modes, we have found a power-law distribution of the motif counts on each motif mode. We postulate that motif modes may very well represent the evolutionary-conserved topological units of a protein interaction network. CONCLUSION: For the first time, the motifs of a protein interaction network have been investigated beyond the scope of motif topology. The motif modes determined in this study have not only enabled us to differentiate among different evolutionary constraints on motifs of the same topology but have also opened up new avenues through which protein interaction networks can be analyzed

A Comparative Study of Three Fecal Occult Blood Tests in Upper Gastrointestinal Bleeding

The purpose of this study was to evaluate the performance characteristics of three fecal occult blood tests (FOBTs): the chemical o-toluidine test, the immunochemical OC-Hemodia test, and the immunochromatographic Quick Chaser Occult Blood (QCOB) test, which detect human hemoglobin and transferrin simultaneously in cases of upper gastrointestinal (GI) bleeding. Included were 48 FOBT specimens in 48 consecutive admission cases of upper GI bleeding (endoscopy confirmed). We excluded those fecal specimens with an obvious tarry and bloody appearance. The QCOB test revealed the highest positive rates of 33/48 (68.8%), and significantly higher positive rates than that of the OC-Hemodia test and o-toluidine test (p< 0.025 and < 0.01, respectively). In the patient group with upper GI bleeding due to gastric and duodenal ulcers, the QCOB test had higher positive rates (68.6%) than did the o-toluidine test (34.3%) (p< 0.01). There was no fecal specimen that was positive for the o-toluidine test or OC-Hemodia test and was negative for the QCOB test. Our results reveal that the QCOB test has significantly higher positive rates of fecal occult blood than either the OC-Hemodia test or o-toluidine test. The QCOB test is better than the other two tests for detecting occult blood in patients with upper GI bleeding

Data from: Genetic relationships and ecological divergence in Salix species and populations in Taiwan

Linking ecology with evolutionary biology is important to understand how environments drive population and species divergence. Phenotypically diverse Salix species, such as lowland riparian willow trees and middle- to high-elevation multistemmed shrubs and alpine dwarf shrubs, provide opportunities for studying genetic divergence driven by ecological factors. We used amplified fragment length polymorphism (AFLP) to quantify the genetic variation of 185 individuals from nine populations of four Salix species in Taiwan. Our phylogenetic analyses distinguished two riparian species and the separation of riparian species from multistemmed and dwarf shrub species. Variance partitioning for the total data found that environment explained a substantially larger proportion of genetic variation than geography. However, no genetic variation was explained by geography alone when only compared within and between species. Spatially structured regional environmental effects explained more variation than pure environments in most comparisons within and between species, suggesting that unmeasured environmental variables and/or past demographic histories played important roles in shaping population and species divergence. Based on forward selection analysis, annual mean temperature, aspect, and fraction of absorbed photosynthetically active radiation were the most influential ecological factors in shaping genetic variation within and between species. Nevertheless, different combinations of environmental variables correlated significantly with genetic variation within and between species. We identified eight AFLP loci that potentially evolved under selection intraspecifically using different outlier detection methods. These loci correlated with more than one environmental variable, suggesting local adaptation along environmental gradients at the population level

Salixaflp

Amplified fragment length polymorphism (AFLP) genotyping data of 185 samples from nine populations of four Taiwanese Salix species and eight samples from six Chinese Salix species

How small is TOO small? New liver constraint is needed- Proton therapy of hepatocellular carcinoma patients with small normal liver.

PURPOSE:This study evaluated the outcomes of hepatocellular carcinoma (HCC) patients with small normal liver volume (NLV) treated with proton beam therapy (PBT) and introduced estimated standard liver volume (eSLV) as a new constraint. MATERIALS AND METHODS:HCC patients with NLV 20% and an rV30/eSLV ratio of >30% are acceptable

Mechanistic Study on Artificial Stabilization of Lithium Metal Anode via Thermal Pyrolysis of Ammonium Fluoride in Lithium Metal Batteries

The use of the “Holy Grail” lithium metal anode is pivotal to achieve superior energy density. However, the practice of a lithium metal anode faces practical challenges due to the thermodynamic instability of lithium metal and dendrite growth. Herein, an artificial stabilization of lithium metal was carried out via the thermal pyrolysis of the NH4F salt, which generates HF­(g) and NH3(g). An exposure of lithium metal to the generated gas induces a spontaneous reaction that forms multiple solid electrolyte interface (SEI) components, such as LiF, Li3N, Li2NH, LiNH2, and LiH, from a single salt. The artificially multilayered protection on lithium metal (AF-Li) sustains stable lithium stripping/plating. It suppresses the Li dendrite under the Li||Li symmetric cell. The half-cell Li||Cu and Li||MCMB systems depicted the attributions of the protective layer. We demonstrate that the desirable protective layer in AF-Li exhibited remarkable capacity retention (CR) results. LiFePO4 (LFP) showed a CR of 90.6% at 0.5 mA cm–2 after 280 cycles, and LiNi0.5Mn0.3Co0.2O2 (NCM523) showed 58.7% at 3 mA cm–2 after 410 cycles. Formulating the multilayered protection, with the simultaneous formation of multiple SEI components in a facile and cost-effective approach from NH4F as a single salt, made the system competent

Prognostic Significance of Primary Tumor Location in Upper Tract Urothelial Carcinoma Treated with Nephroureterectomy: A Retrospective, Multi-Center Cohort Study in Taiwan

We sought to examine the effect of tumor location on the prognosis of patients with upper tract urothelial carcinoma (UTUC) treated with radical nephroureterectomy (RNU). This retrospective study came from the Taiwan UTUC Collaboration Group, which consisted of 2658 patients at 15 institutions in Taiwan from 1988 to 2019. Patients with kidney-sparing management, both renal pelvic and ureteral tumors, as well as patients lacking complete data were excluded; the remaining 1436 patients were divided into two groups: renal pelvic tumor (RPT) and ureteral tumor (UT), with 842 and 594 patients, respectively. RPT was associated with more aggressive pathological features, including higher pathological T stage (p &lt; 0.001) and the presence of lymphovascular invasion (p = 0.002), whereas patients with UT often had synchronous bladder tumor (p &lt; 0.001), and were more likely to bear multiple lesions (p = 0.001). Our multivariate analysis revealed that UT was a worse prognostic factor compared with RPT (overall survival: HR 1.408, 95% CI 1.121&ndash;1.767, p = 0.003; cancer-specific survival: HR 1.562, 95% CI 1.169&ndash;2.085, p = 0.003; disease-free survival: HR 1.363, 95% CI 1.095&ndash;1.697, p = 0.006; bladder-recurrence-free survival: HR 1.411, 95% CI 1.141&ndash;1.747, p = 0.002, respectively). Based on our findings, UT appeared to be more malignant and had a worse prognosis than RPT

Prophylaxis for paediatric emergence delirium in desflurane-based anaesthesia: a network meta-analysis

Purpose: The prevalence of postoperative emergence delirium in paediatric patients (pedED) following desflurane anaesthesia is considerably high at 50–80%. Although several pharmacological prophylactic strategies have been introduced to reduce the risk of pedED, conclusive evidence about the superiority of these individual regimens is lacking. The aim of the current study was to assess the potential prophylactic effect and safety of individual pharmacotherapies in the prevention of pedED following desflurane anaesthesia.Methods: This frequentist model network meta-analysis (NMA) of randomized controlled trials (RCTs) included peer-reviewed RCTs of either placebo-controlled or active-controlled design in paediatric patients under desflurane anaesthesia.Results: Seven studies comprising 573 participants were included. Overall, the ketamine + propofol administration [odds ratio (OR) = 0.05, 95% confidence intervals (95%CIs) 0.01–0.33], dexmedetomidine alone (OR = 0.13, 95%CIs 0.05–0.31), and propofol administration (OR = 0.30, 95%CIs 0.10–0.91) were associated with a significantly lower incidence of pedED than the placebo/control groups. In addition, only gabapentin and dexmedetomidine were associated with a significantly higher improvement in the severity of emergence delirium than the placebo/control groups. Finally, the ketamine + propofol administration was associated with the lowest incidence of pedED, whereas gabapentin was associated with the lowest severity of pedED among all of the pharmacologic interventions studied.Conclusions: The current NMA showed that ketamine + propofol administration was associated with the lowest incidence of pedED among all of the pharmacologic interventions studied. Future large-scale trials to more fully elucidate the comparative benefits of different combination regimens are warranted.</p