Gauss decomposition for Chevalley groups, revisited

In the 1960's Noboru Iwahori and Hideya Matsumoto, Eiichi Abe and Kazuo Suzuki, and Michael Stein discovered that Chevalley groups $G=G(\Phi,R)$ over a semilocal ring admit remarkable Gauss decomposition $G=TUU^-U$, where $T=T(\Phi,R)$ is a split maximal torus, whereas $U=U(\Phi,R)$ and $U^-=U^-(\Phi,R)$ are unipotent radicals of two opposite Borel subgroups $B=B(\Phi,R)$ and $B^-=B^-(\Phi,R)$ containing $T$. It follows from the classical work of Hyman Bass and Michael Stein that for classical groups Gauss decomposition holds under weaker assumptions such as \sr(R)=1 or \asr(R)=1. Later the second author noticed that condition \sr(R)=1 is necessary for Gauss decomposition. Here, we show that a slight variation of Tavgen's rank reduction theorem implies that for the elementary group $E(\Phi,R)$ condition \sr(R)=1 is also sufficient for Gauss decomposition. In other words, $E=HUU^-U$, where $H=H(\Phi,R)=T\cap E$. This surprising result shows that stronger conditions on the ground ring, such as being semi-local, \asr(R)=1, \sr(R,\Lambda)=1, etc., were only needed to guarantee that for simply connected groups $G=E$, rather than to verify the Gauss decomposition itself

Pigmentation and TYRP1 expression are mediated by zinc through the early secretory pathway-resident ZNT proteins

メラニン生合成には、亜鉛も必要だった！. 京都大学プレスリリース. 2023-04-19.Tyrosinase (TYR) and tyrosinase-related proteins 1 and 2 (TYRP1 and TYRP2) are essential for pigmentation. They are generally classified as type-3 copper proteins, with binuclear copper active sites. Although there is experimental evidence for a copper cofactor in TYR, delivered via the copper transporter, ATP7A, the presence of copper in TYRP1 and TYRP2 has not been demonstrated. Here, we report that the expression and function of TYRP1 requires zinc, mediated by ZNT5–ZNT6 heterodimers (ZNT5–6) or ZNT7–ZNT7 homodimers (ZNT7). Loss of ZNT5–6 and ZNT7 function results in hypopigmentation in medaka fish and human melanoma cells, and is accompanied by immature melanosomes and reduced melanin content, as observed in TYRP1 dysfunction. The requirement of ZNT5–6 and ZNT7 for TYRP1 expression is conserved in human, mouse, and chicken orthologs. Our results provide novel insights into the pigmentation process and address questions regarding metalation in tyrosinase protein family

Development and Validation of Cutoff Value for Reduced Muscle Mass for GLIM Criteria in Patients with Gastrointestinal and Hepatobiliary–Pancreatic Cancers

The Global Leadership Initiative on Malnutrition (GLIM) criteria recommends using race- and sex-adjusted cutoff values for reduced muscle mass (RMM), but the only cutoff values available for Asians are the skeletal muscle mass index (SMI) established by the Asian Working Group for Sarcopenia (AWGS). This retrospective study aimed to develop and validate cutoff values for the fat-free mass index (FFMI) and arm circumference (AC) of Asians, and to investigate the association between GLIM malnutrition and prognosis. A total of 660 patients with primary gastrointestinal (GI) and hepatobiliary–pancreatic (HBP) cancers who underwent their first resection surgery were recruited and randomly divided into development and validation groups. The FFMI and AC cutoff values were calculated by receiver operating characteristic curve analysis for the AWGS SMI as the gold standard. The cutoff values for each RMM were used to diagnose malnutrition on the basis of GLIM criteria, and the survival rates were compared. The optimal FFMI cutoff values for RMM were 17 kg/m2 for men and 15 kg/m2 for women, and for AC were 27 cm for men and 25 cm for women. In the validation group, the accuracy of the FFMI and AC cutoff values to discriminate RMM were 85.2% and 68.8%, respectively. Using any of the three measures of RMM, overall survival rates were significantly lower in the GLIM malnutrition group. In conclusion, the cutoff values for the FFMI and AC in this study could discriminate RMM, and GLIM malnutrition using these cutoff values was associated with decreased survival

Impact of phase angle on postoperative prognosis

Objective Phase angle (PhA), by bioelectrical impedance analysis, has been used in patients with several diseases; however, its prognostic value in patients with gastrointestinal and hepatobiliary–pancreatic (HBP) cancer is unclear. The present study aimed to investigate the impact of PhA on postoperative short-term outcomes and long-term survival in these patients. Research Methods & Procedures This retrospective study reviewed data of 501 patients with gastrointestinal and HBP cancers who underwent first resection surgery and divided the data into the following groups according to the preoperative PhA quartile values by sex: high-PhA group with the highest quartile (Q4), normal-PhA group with middle quartiles (Q3 and Q2), and low-PhA group with the lowest quartile (Q1). Preoperative nutritional statuses, postoperative short-term outcomes during hospitalization, and 5-year survival between three groups were compared. Cox proportional hazard models were used to evaluate the prognostic effect of PhA. Results PhA positively correlated with body weight, skeletal muscle mass, and handgrip strength, and negatively correlated with age and C-reactive protein levels. The low-PhA group showed a high prevalence of malnutrition (48%) than normal-PhA (25%), and high-PhA (9%) (P < 0.001). The incidence of postoperative severe complications was 10% in all patients [14% in low-PhA, 12% in normal-PhA, and 4% in high-PhA (P = 0.018)]. The incidence of prolonged postoperative high care unit or/and intensive care unit stays was 8% in all patients [16% in low-PhA, 8% in normal-PhA, and 2% in high-PhA (P < 0.001)]. The 5-year survival rate was 74% in all patients [68% in low-PhA, 74% in normal-PhA, and 79% in high-PhA (P < 0.001)]. The multivariate analysis demonstrated that a low-PhA group was an independent risk factor for mortality (hazard ratio, 1.99; 95% confidence interval 1.05–3.90; P = 0.034). Conclusion PhA is a useful short-term and long-term postoperative prognostic marker for patients with gastrointestinal and HBP cancers

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes

<p>Abstract</p> <p>Background</p> <p>As larger datasets are produced with the development of genome-scale experimental techniques, it has become essential to explicitly describe the meta-data (information describing the data) generated by an experiment. The experimental process is a part of the meta-data required to interpret the produced data, and SDRF (Sample and Data Relationship Format) supports its description in a spreadsheet or tab-delimited file. This format was primarily developed to describe microarray studies in MAGE-tab, and it is being applied in a broader context in ISA-tab. While the format provides an explicit framework to describe experiments, increase of experimental steps makes it less obvious to understand the content of the SDRF files.</p> <p>Results</p> <p>Here, we describe a new tool, SDRF2GRAPH, for displaying experimental steps described in an SDRF file as an investigation design graph, a directed acyclic graph representing experimental steps. A spreadsheet, in Microsoft Excel for example, which is used to edit and inspect the descriptions, can be directly input via a web-based interface without converting to tab-delimited text. This makes it much easier to organize large contents of SDRF described in multiple spreadsheets.</p> <p>Conclusion</p> <p>SDRF2GRAPH is applicable for a wide range of SDRF files for not only microarray-based analysis but also other genome-scale technologies, such as next generation sequencers. Visualization of the Investigation Design Graph (IDG) structure leads to an easy understanding of the experimental process described in the SDRF files even if the experiment is complicated, and such visualization also encourages the creation of SDRF files by providing prompt visual feedback.</p

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

The international Functional Annotation Of the Mammalian Genomes 4 (FANTOM4) research collaboration set out to better understand the transcriptional network that regulates macrophage differentiation and to uncover novel components of the transcriptome employing a series of high-throughput experiments. The primary and unique technique is cap analysis of gene expression (CAGE), sequencing mRNA 5′-ends with a second-generation sequencer to quantify promoter activities even in the absence of gene annotation. Additional genome-wide experiments complement the setup including short RNA sequencing, microarray gene expression profiling on large-scale perturbation experiments and ChIP-chip for epigenetic marks and transcription factors. All the experiments are performed in a differentiation time course of the THP-1 human leukemic cell line. Furthermore, we performed a large-scale mammalian two-hybrid (M2H) assay between transcription factors and monitored their expression profile across human and mouse tissues with qRT-PCR to address combinatorial effects of regulation by transcription factors. These interdependent data have been analyzed individually and in combination with each other and are published in related but distinct papers. We provide all data together with systematic annotation in an integrated view as resource for the scientific community (http://fantom.gsc.riken.jp/4/). Additionally, we assembled a rich set of derived analysis results including published predicted and validated regulatory interactions. Here we introduce the resource and its update after the initial releas

Malnutrition by European Society for Clinical Nutrition and Metabolism criteria predicts prognosis in patients with gastrointestinal and hepatobiliary–pancreatic cancer

Background & Aims: The European Society for Clinical Nutrition and Metabolism (ESPEN) proposed the ESPEN diagnostic criteria (EDC) for malnutrition in 2015. There is no report on the association between the EDC and prognosis in patients with gastrointestinal (GI) and hepatobiliary–pancreatic (HBP) cancer. This study aimed to (1) determine the prevalence of EDC malnutrition, (2) investigate the validity of the EDC as a nutritional and prognostic indicator, and (3) examine which components of the EDC are most related to long-term prognosis in patients with GI and HBP cancers. Methods: A total of 634 patients with primary GI and HBP cancers who underwent their first resection surgery between July 2014 and March 2018 were retrospectively recruited. According to the EDC, patients were divided into malnourished and non-malnourished groups. Clinical parameters and survival between these two groups were compared. The prognostic effects of the EDC and the EDC components were analyzed using Cox proportional hazard models. Results: The prevalence of EDC malnutrition was 22%. Anthropometric data and biochemical data were associated with EDC malnutrition. The 5-year survival rate was lower in the malnourished group (72%) than in the non-malnourished group (73%; P = 0.007). The multivariate analysis demonstrated that the malnourished group was an independent risk factor for mortality (hazard ratio = 1.70 in the malnourished group; 95% confidence interval 1.08–2.63; P = 0.024). Among EDC components, body mass index (BMI) of <18.5 kg/m2 was an independent poor prognostic factor. Conclusions: EDC malnutrition is associated with poor postoperative long-term prognosis. Among the EDC components, BMI of <18.5 kg/m2 is most associated with prognosis in patients with preoperative GI and HBP cancers

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation

Transcriptional Regulatory Networks (TRNs) coordinate multiple transcription factors (TFs) in concert to maintain tissue homeostasis and cellular function. The re-establishment of target cell TRNs has been previously implicated in direct trans-differentiation studies where the newly introduced TFs switch on a set of key regulatory factors to induce de novo expression and function. However, the extent to which TRNs in starting cell types, such as dermal fibroblasts, protect cells from undergoing cellular reprogramming remains largely unexplored. In order to identify TFs specific to maintaining the fibroblast state, we performed systematic knockdown of 18 fibroblast-enriched TFs and analyzed differential mRNA expression against the same 18 genes, building a Matrix-RNAi. The resulting expression matrix revealed seven highly interconnected TFs. Interestingly, suppressing four out of seven TFs generated lipid droplets and induced PPARG and CEBPA expression in the presence of adipocyte-inducing medium only, while negative control knockdown cells maintained fibroblastic character in the same induction regime. Global gene expression analyses further revealed that the knockdown-induced adipocytes expressed genes associated with lipid metabolism and significantly suppressed fibroblast genes. Overall, this study reveals the critical role of the TRN in protecting cells against aberrant reprogramming, and demonstrates the vulnerability of donor cell's TRNs, offering a novel strategy to induce transgene-free trans-differentiations

Prolactin inhibits osteoclastic activity in the goldfish scale: A novel direct action of prolactin in teleosts

In teleosts, prolactin is involved in calcium regulation, but its role in scale/bone metabolism Is unclear. Using the in-vitro system with goldfish scales developed recently, we explored the effects of teleost prolactin, growth hormone, and somatolactin on osteoclasts and osteoblasts. Addition of prolactin at concentrations of 0.01-100 ng/ml reduced osteoclastic activity, partly via osteoclast apoptosis, after 6-18 h incubation. Conversely, growth hormone and somatolactin at a concentration of 100 ng/ml increased osteoclastic activity after 18 h incubation, indicating the specificity of the inhibitory effect of prolactin on osteoclastic activity. On the other hand, these three hormones promoted osteoblastic activity at concentrations of 10-100 ng/ml. The results from this study are the first demonstration of direct effects of prolactin on scale/bone metabolism and osteoclastic activity in a teleost. © 2008 Zoological Society of Japan