Developing New Oligo Probes to Distinguish Specific Chromosomal Segments and the A, B, D Genomes of Wheat (Triticum aestivum L.) Using ND-FISH

Non-denaturing FISH (ND-FISH) technology has been widely used to study the chromosomes of Triticeae species because of its convenience. The oligo probes for ND-FISH analysis of wheat (Triticum aestivum L.) chromosomes are still limited. In this study, the whole genome shotgun assembly sequences (IWGSC WGA v0.4) and the first version of the reference sequences (IWGSC RefSeq v1.0) of Chinese Spring (T. aestivum L.) were used to find new tandem repeats. One hundred and twenty oligo probes were designed according to the new tandem repeats and used for ND-FISH analysis of chromosomes of wheat Chinese Spring. Twenty nine of the 120 oligo probes produce clear or strong signals on wheat chromosomes. Two of the 29 oligo probes can be used to conveniently distinguish wheat A-, B-, and D-genome chromosomes. Sixteen of the 29 oligo probes only produce clear or strong signals on the subtelomeric regions of 1AS, 5AS, 7AL, 4BS, 5BS, and 3DS arms, on the telomeric regions of 1AL, 5AL, 2BS, 3BL, 6DS, and 7DL arms, on the intercalary regions of 4AL and 2DL arms, and on the pericentromeric regions of 3DL and 6DS arms. Eleven of the 29 oligo probes generate distinct signal bands on several chromosomes and they are different from those previously reported. In addition, the short and long arms of 6D chromosome have been confirmed. The new oligo probes developed in this study are useful and convenient for distinguishing wheat chromosomes or specific segments of wheat chromosomes

Development and external validation of a nomogram for predicting postoperative pneumonia in aneurysmal subarachnoid hemorrhage

BackgroundPostoperative pneumonia (POP) is a common complication after aneurysmal subarachnoid hemorrhage (aSAH) associated with increased mortality rates, prolonged hospitalization, and high medical costs. It is currently understood that identifying pneumonia early and implementing aggressive treatment can significantly improve patients' outcomes. The primary objective of this study was to explore risk factors and develop a logistic regression model that assesses the risks of POP.MethodsAn internal cohort of 613 inpatients with aSAH who underwent surgery at the Neurosurgical Department of First Affiliated Hospital of Wenzhou Medical University was retrospectively analyzed to develop a nomogram for predicting POP. We assessed the discriminative power, accuracy, and clinical validity of the predictions by using the area under the receiver operating characteristic curve (AUC), the calibration curve, and decision curve analysis (DCA). The final model was validated using an external validation set of 97 samples from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database.ResultsAmong patients in our internal cohort, 15.66% (n = 96/613) of patients had POP. The least absolute shrinkage and selection operator (LASSO) regression analysis identified the Glasgow Coma Scale (GCS), mechanical ventilation time (MVT), albumin, C-reactive protein (CRP), smoking, and delayed cerebral ischemia (DCI) as potential predictors of POP. We then used multivariable logistic regression analysis to evaluate the effects of these predictors and create a final model. Eighty percentage of patients in the internal cohort were randomly assigned to the training set for model development, while the remaining 20% of patients were allocated to the internal validation set. The AUC values for the training, internal, and external validation sets were 0.914, 0.856, and 0.851, and the corresponding Brier scores were 0.084, 0.098, and 0.143, respectively.ConclusionWe found that GCS, MVT, albumin, CRP, smoking, and DCI are independent predictors for the development of POP in patients with aSAH. Overall, our nomogram represents a reliable and convenient approach to predict POP in the patient population

Re-ID done right: towards good practices for person re-identification

Training a deep architecture using a ranking loss has become standard for the person re-identification task. Increasingly, these deep architectures include additional components that leverage part detections, attribute predictions, pose estimators and other auxiliary information, in order to more effectively localize and align discriminative image regions. In this paper we adopt a different approach and carefully design each component of a simple deep architecture and, critically, the strategy for training it effectively for person re-identification. We extensively evaluate each design choice, leading to a list of good practices for person re-identification. By following these practices, our approach outperforms the state of the art, including more complex methods with auxiliary components, by large margins on four benchmark datasets. We also provide a qualitative analysis of our trained representation which indicates that, while compact, it is able to capture information from localized and discriminative regions, in a manner akin to an implicit attention mechanism

Pushing the Limits of Machine Design: Automated CPU Design with AI

Design activity -- constructing an artifact description satisfying given goals and constraints -- distinguishes humanity from other animals and traditional machines, and endowing machines with design abilities at the human level or beyond has been a long-term pursuit. Though machines have already demonstrated their abilities in designing new materials, proteins, and computer programs with advanced artificial intelligence (AI) techniques, the search space for designing such objects is relatively small, and thus, "Can machines design like humans?" remains an open question. To explore the boundary of machine design, here we present a new AI approach to automatically design a central processing unit (CPU), the brain of a computer, and one of the world's most intricate devices humanity have ever designed. This approach generates the circuit logic, which is represented by a graph structure called Binary Speculation Diagram (BSD), of the CPU design from only external input-output observations instead of formal program code. During the generation of BSD, Monte Carlo-based expansion and the distance of Boolean functions are used to guarantee accuracy and efficiency, respectively. By efficiently exploring a search space of unprecedented size 10^{10^{540}}, which is the largest one of all machine-designed objects to our best knowledge, and thus pushing the limits of machine design, our approach generates an industrial-scale RISC-V CPU within only 5 hours. The taped-out CPU successfully runs the Linux operating system and performs comparably against the human-designed Intel 80486SX CPU. In addition to learning the world's first CPU only from input-output observations, which may reform the semiconductor industry by significantly reducing the design cycle, our approach even autonomously discovers human knowledge of the von Neumann architecture.Comment: 28 page

Resistance to preservatives and the viable but non-culturable state formation of Asaia lannensis in flavored syrups

Food security is a crucial issue that has caused extensive concern, and the use of food flavors has become prevalent over time. we used the molecular biological techniques, preservative susceptibility testing, viable but non-culturable (VBNC) state induction testing, and a transcriptome analysis to examine the bacterial contamination of favored syrup and identify the causes and develop effective control measures. The results showed that Asaia lannensis WLS1-1 is a microorganism that can spoil food and is a member of the acetic acid bacteria families. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests showed that WLS1-1 was susceptible to potassium sorbate (PS), sodium benzoate (SB), and sodium sulffte (SS) at pH 4.0. It revealed a progressive increase in resistance to these preservatives at increasing pH values. WLS1-1 was resistant to PS, SB and SS with an MIC of 4.0, 2.0 and 0.5  g/L at pH 5.0, respectively. The MIC values exceed the maximum permissible concentrations that can be added. The induction test of the VBNC state demonstrated that WLS1-1 lost its ability to grow after 321 days of PS induction, 229  days of SB induction and 52  days of SS induction combined with low temperature at 4°C. Additionally, laser confocal microscopy and a propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assay showed that WLS1-1 was still alive after VBNC formation. There were 7.192 ± 0.081 (PS), 5.416 ± 0.149 (SB) and 2.837 ± 0.134 (SS) log10(CFU/mL) of viable bacteria. An analysis of the transcriptome data suggests that Asaia lannensis can enter the VBNC state by regulating oxidative stress and decreasing protein synthesis and metabolic activity in response to low temperature and preservatives. The relative resistance of Asaia lannensis to preservatives and the induction of the VBNC state by preservatives are the primary factors that contribute to the contamination of favored syrup by this bacterium. To our knowledge, this study represents the first evidence of the ability of Asaia lannensis to enter the VBNC state and provides a theoretical foundation for the control of organisms with similar types of activity

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Study on New Strategy toward Gold(I/III) Redox Catalysis

This dissertation mainly contains three parts: 1) the study of ligand assisted gold oxidative addition toward aryl iodide to achieve the alkene difunctionalization. 2) The selective arylation reaction via electrochemical anode oxidation promoted gold redox chemistry. 3) The π acid reactivity of gold redox chemistry under electrochemistry conditions. In the first part, the gold-catalyzed intermolecular oxyarylation of alkene is reported. This work employed the oxidative addition of aryl iodide to Me-DalphosAu+ for the formation of Au(III)-Ar intermediate. The better binding ability of alkene over O nucleophiles ensured the success of intermolecular oxyarylation, giving desired products with broad substrate scope and high efficiency. “One-pot” converting of methoxy group into other nucleophiles allowed achieving alkene difunctionalization with C-N, C-S, and C-C bonds construction under mild conditions. In the second part, The combination of ArB(OH)2 transmetallation with cationic gold(I) [LAu]+ and electrochemical anodic oxidation (EAO) approach was successfully developed for the preparation of AuIII-Ar intermediate for the first time. This in-situ generated aryl gold intermediate gave rapid and controllable transmetallation with ArB(OH)2 or alkyne followed by reductive elimination to generate either di-aryl coupling or sp2-sp Sonogashira-type coupling products under mild conditions with no need of external oxidants. This study significantly extended the versatility of electrochemical approach in promoting gold redox catalysis. In the third part, the combination of gold π acid reactivity and electrochemical anode oxidation promoted gold(I/III) redox catalysis was reported for the first time. With the utility of aryl hydrazine HOTf salt as carbon source, we avoided the generation of reactive L-Au(I)-Ar intermediate in the reaction pathway. The reaction was successfully carried out under mild conditions without any external oxidant, and both alkene and alkyne di-functionalization were received under mild conditions with excellent functional group compatibility and regioselectivity. In summary, we explored two new strategies for achieving gold redox chemistry in a catalytic version. Both the oxidative addition approach and the electrochemistry oxidation pathway showed excellent reactivity under mild conditions and have a broad substrate scope. These newly developed strategy will definitely facilitate more useful transformations in gold redox chemistry

Study on New Strategy toward Gold(I/III) Redox Catalysis

This dissertation mainly contains three parts: 1) the study of ligand assisted gold oxidative addition toward aryl iodide to achieve the alkene difunctionalization. 2) The selective arylation reaction via electrochemical anode oxidation promoted gold redox chemistry. 3) The π acid reactivity of gold redox chemistry under electrochemistry conditions. In the first part, the gold-catalyzed intermolecular oxyarylation of alkene is reported. This work employed the oxidative addition of aryl iodide to Me-DalphosAu+ for the formation of Au(III)-Ar intermediate. The better binding ability of alkene over O nucleophiles ensured the success of intermolecular oxyarylation, giving desired products with broad substrate scope and high efficiency. “One-pot” converting of methoxy group into other nucleophiles allowed achieving alkene difunctionalization with C-N, C-S, and C-C bonds construction under mild conditions. In the second part, The combination of ArB(OH)2 transmetallation with cationic gold(I) [LAu]+ and electrochemical anodic oxidation (EAO) approach was successfully developed for the preparation of AuIII-Ar intermediate for the first time. This in-situ generated aryl gold intermediate gave rapid and controllable transmetallation with ArB(OH)2 or alkyne followed by reductive elimination to generate either di-aryl coupling or sp2-sp Sonogashira-type coupling products under mild conditions with no need of external oxidants. This study significantly extended the versatility of electrochemical approach in promoting gold redox catalysis. In the third part, the combination of gold π acid reactivity and electrochemical anode oxidation promoted gold(I/III) redox catalysis was reported for the first time. With the utility of aryl hydrazine HOTf salt as carbon source, we avoided the generation of reactive L-Au(I)-Ar intermediate in the reaction pathway. The reaction was successfully carried out under mild conditions without any external oxidant, and both alkene and alkyne di-functionalization were received under mild conditions with excellent functional group compatibility and regioselectivity. In summary, we explored two new strategies for achieving gold redox chemistry in a catalytic version. Both the oxidative addition approach and the electrochemistry oxidation pathway showed excellent reactivity under mild conditions and have a broad substrate scope. These newly developed strategy will definitely facilitate more useful transformations in gold redox chemistry