First Report of Root Rot on Rhizome of Polygonatum kingianum Caused by Aspergillus awamori.

Polygonatum kingianum Coll. et Hemsl (Huangjing), which belongs to the family Asparagaceae, is a perennial traditional Chinese herb with homologous medicinal and edible value (Liu et al., 2021). Huangjing is known to promote blood circulation; it has anti-inflammatory properties, increases immunity, and provides hypoglycemic treatments (Ma et al., 2019). Root rot-infected P. kingianum exhibited withering yellow leaves and stems, rhizome rot, slowed growth, and plant death. In recent years, with an average incidence of up to 45%, the spread of HJ root rot (rhizome and stem bases) has resulted in a significant reduction in the quality and up to 63% reduction in the yields of Sichuan Junlian (104.5°E, 28.2°N) and Guizhou Zhunyi (107.0°E, 27.7°N). After collecting the diseased samples, we used the tissue isolation method to isolate the pathogenic fungi (Wu et al., 2020). Four fungal isolates associated with root rot were obtained: HJ-G2 (two strains), HJ-G3 (one strain), HJ-G4 (one strain), and HJ-G6 (two strains), of which HJ-G2 and HJ-G6 were the dominant species. To determine pathogenicity of each strain, tests were conducted by wounding rhizomes wth an inoculation needle and the pathogen strain was inoculated onto the wound and symptoms observed. The results reveal that HJ-G6 exhibited the strongest pathogenicity against P. kingianum (Figure 1). The HJ-G6 colonies were black, grew rapidly, and produced a large number of spores (Figure 1). A spherical apical sac (conidial head) is formed at the top with two palisades of cells, metulae and phialides, which are shaped radially and produce a large number of spores with 2-5 um in diameter (Figure 2). Morphological observations revealed that the isolate was consistent with Aspergillus awamori (Naher et al., 2021). To further confirm the fungal species, the ribosomal internal transcribed spacer (ITS), ß-tubulin (TUB), and elongation factor 1-alpha (EF-1a) gene regions were amplified with ITS1/ITS4, Bt2a/ Bt2b, and EF1/EF2. Primer and PCR amplification were performed as previously described (Paul et al., 2017). The sequences were compared with those obtained from GenBank. The ITS sequences (GenBank accession number OR682143) of the isolates (HJ-G6) were 100% identical to those of the strain PANCOM10 (GenBank accession number MT007535.1) of Aspergillus awamori. The EF-1a sequences (GenBank accession OR752352) of the isolates (HJ-G6) were 98% identical with strain ITEM 4777 (GenBank accession FN665402.1) of Aspergillus awamori. The TUB sequences (GenBank accession number OR752351) of the isolate (HJ-G6) were 100% identical with strain AF158 (GenBank accession MH781275.1) of Aspergillus awamori. Three maximum likelihood trees were constructed using MEGA v5.0 (Kumar et al., 2018) based on the sequences (ITS, TUB, and EF-1a) of the HJ-G6 strain and that of Aspergillus spp. previously deposited in GenBank (Paul et al., 2017). Phylogenetic analysis showed that HJ-G6 belonged to the Aspergillus awamori clade (Figure 3). Combined with morphological analysis and DNA sequencing, HJ-G6 was identified as Aspergillus awamori. To verify pathogenicity, P. kingianum roots were inoculated with the colonized agar discs of the isolates. P. kingianum plants inoculated with uncolonized agar discs were used as controls. After inoculation, P. kingianum roots were moved to the inoculation chamber under high humidity at 28 °C for 1 d and then transferred to a greenhouse. Previous studies have reported that Fusarium sp. are root rot pathogens in the rhizomes of medicinal plants (Pang et al., 2022; Song et al., 2023). In this study, HJ-G2, HJ-G3, and HJ-G4 were used as the positive controls. Typical symptoms of root rot appeared 3 days after inoculation and were similar to those observed in the field, whereas the control plants remained symptomless. According to the results of the inoculation experiment, the pathogenicity of Aspergillus awamori to P. kingianum root rot was significantly stronger than that of Fusarium (Figure 1). The pathogen was isolated from the rotting root of P. kingianum and the ITS region was sequenced again. Alignment analysis of the ITS sequences revealed that the causal agents were consistent with those of the original isolates. These studies fulfill Koch's postulates. As far as we know, this is the first report of Aspergillus awamori causing root rot in P. kingianum.

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae.

Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.

Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction.

MOTIVATION: Personalized cancer treatments require accurate drug response predictions. Existing deep learning methods show promise but higher accuracy is needed to serve the purpose of precision medicine. The prediction accuracy can be improved with not only topology but geometrical information of drugs. RESULTS: A novel deep learning methodology for drug response prediction is presented, named Hi-GeoMVP. It synthesizes hierarchical drug representation with multi-omics data, leveraging graph neural networks and variational autoencoders for detailed drug and cell line representations. Multi-task learning is employed to make better prediction, while both 2D and 3D molecular representations capture comprehensive drug information. Testing on the GDSC dataset confirms Hi-GeoMVP's enhanced performance, surpassing prior state-of-the-art methods by improving the Pearson correlation coefficient from 0.934 to 0.941 and decreasing the root mean square error from 0.969 to 0.931. In the case of blind test, Hi-GeoMVP demonstrated robustness, outperforming the best previous models with a superior Pearson correlation coefficient in the drug-blind test. These results underscore Hi-GeoMVP's capabilities in drug response prediction, implying its potential for precision medicine. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/matcyr/Hi-GeoMVP.

Freezing pre-treatment improves radio frequency explosion puffing (RFEP) quality by altering the cellular structure of purple sweet potato [Ipomoea batatas (L) Lam.].

Radio frequency explosion puffing (RFEP) is a novel oil-free puffing technique used to produce crispy textured and nutritious puffed snacks. This study aimed to investigate the effects of freezing at different temperatures (-20 °C, -40 °C, -80 °C) for14 h and freezing times (1 and 2 times) on the cellular structure of purple sweet potato and the quality of RFEP chips. The analysis of cell microstructure, conductivity, and rheology revealed that higher freezing temperatures and more freezing times resulted in increased damage to the cellular structure, leading to greater cell membrane permeability and decreased cell wall stiffness. However, excessive damage to cellular structure caused tissue structure to collapse. Compared with the control group (4 °C), the RFEP sample pre-frozen once at -40 °C had a 47.13 % increase in puffing ratio and a 61.93 % increase in crispness, while hardness decreased by 23.44 % (p < 0.05). There was no significant change in anthocyanin retention or color difference. X-ray microtomography demonstrated that the RFEP sample pre-frozen once at -40 °C exhibited a more homogeneous morphology and uniform pore distribution, resulting in the highest overall acceptability. In conclusion, freezing pre-treatment before RFEP can significantly enhance the puffing quality, making this an effective method for preparing oil-free puffing products for fruits and vegetables.

Vertical variation of source-apportioned PM2.5 and selected volatile organic compounds near an elevated expressway in an urban area.

Fine particulate matter (PM2.5) and volatile organic compounds (VOCs) are associated with adverse health effects and show spatial variation in three dimensions. The present study attempted to evaluate source contributions of PM2.5 and toxic VOCs in a metropolitan area focusing on the associated vertical variations. A special emphasis is put on the effects of the elevated expressway on the vertical variability of contribution estimates of the identified sources. Nine source factors, i.e., soil dust, sea salt/oil combustion, secondary nitrate, industrial emission, aged VOCs/secondary aerosol, traffic-related I, solvent use/industrial process, secondary sulfate, and traffic-related II, were identified using positive matrix factorization (PMF). The main contributors to PM2.5 were secondary sulfate (19.1%) and traffic-related emissions (traffic-related I and II, 16.1%), whereas the largest contributors to VOCs were traffic-related emissions (37.6%). The influence of the elevated expressway is suggested to be particularly critical on vertical variations of traffic-related emissions, including aging and secondary formation of locally accumulated air pollutants near roads. Increasing the building porosity under the viaduct could reduce the accumulation of air pollutants caused by the shelter effect. Additionally, in-street barriers would be beneficial in reducing population exposure to traffic-related emissions by altering the airflows near roads.

Rattan Pepper Polysaccharide Regulates DSS-Induced Intestinal Inflammation and Depressive Behavior through Microbiota-Gut-Brain Axis.

Inflammatory bowel disease (IBD) is a chronic and recurrent disease. Increasing evidence suggests a higher incidence of depression in IBD patients compared with the general population, but the underlying mechanism remains uncertain. Rattan pepper polysaccharide (RPP) is an important active ingredient of rattan pepper, yet its effects and mechanisms on intestinal inflammation and depression-like behavior remain largely unknown. This study aims to investigate the ameliorating effect of RPP on dextran sulfate sodium salt (DSS)-induced intestinal inflammation and depression-like behavior as well as to reveal its mechanism. Our results indicate that RPP effectively ameliorated intestinal microbiota imbalance and metabolic disorders of short-chain fatty acids (SCFAs) and bile acids in mice with DSS-induced inflammation, contributing to the recovery of intestinal Th17/Treg homeostasis. Importantly, RPP effectively alleviated brain inflammation caused by intestinal inflammatory factors entering the brain through the blood-brain barrier. This effect may be attributed to the inhibition of the TLR4/NF-κB signaling pathway, which alleviates neuroinflammation, and the activation of the CREB/BDNF signaling pathway, which improves synaptic dysfunction. Therefore, our findings suggest that RPP may play a role in alleviating DSS-induced gut inflammation and depression-like behavior through the microbiota-gut-brain axis.

More Efficient Approach: Independent Diagnostic Value of Audiovisual Sexual Stimulation for Psychogenic Erectile Dysfunction.

The diagnostic value of audiovisual sexual stimulation (AVSS) for psychogenic erectile dysfunction (ED) is still unclear. We investigated the independent diagnostic value and optimal cut-off parameter of AVSS for psychogenic ED. All participants had received the AVSS test and nocturnal penile tumescence and rigidity (NPTR) monitoring at least twice. ED patients were divided into psychogenic ED and organic ED according to NPTR examination. The diagnostic accuracy of AVSS parameters was evaluated with the receiver operating characteristic (ROC) curve, and the Youden index was employed to determine the optimal diagnostic cut-off values. A total of 346 patients with ED and 60 healthy men were included in this study, among which 162 and 184 cases of psychogenic and organic ED were identified based on NPTR, respectively. When comparing the two ED groups, the area under the curve (AUC) of AVSS parameters was 0.85-0.89. Six-selected AVSS parameters could precisely diagnose psychogenic ED, exhibiting increased diagnostic specificity compared with corresponding sensitivity. When comparing psychogenic ED with the control group, the AUC of the tumescence of the tip was superior to the AUC other parameters (0.81 vs. 0.58, 0.66, 0.59, 0.53, 0.68), and the best determined diagnostic cut-off value was the tumescence of the tip < 29.87%. Independent AVSS could diagnose psychogenic ED objectively and effectively, and its diagnostic value was highest when 1.50% ≤ tumescence of the tip < 29.87%.

Analysis of clinicopathological features and prognostic factors of breast cancer brain metastasis.

BACKGROUND: Breast cancer (BC) has become the most common malignancy in women. The incidence and detection rates of BC brain metastasis (BCBM) have increased with the progress of imaging, multidisciplinary treatment techniques and the extension of survival time of BC patients. BM seriously affects the quality of life and sur-vival prognosis of BC patients. Therefore, clinical research on the clinicopathological features and prognostic factors of BCBM is valuable. By analyzing the clinicopathological parameters of BCBM patients, and assessing the risk factors and prognostic indicators, we can perform hierarchical diagnosis and treatment on the high-risk population of BCBM, and achieve clinical benefits of early diagnosis and treatment. AIM: To explore the clinicopathological features and prognostic factors of BCBM, and provide references for diagnosis, treatment and management of BCBM. METHODS: The clinicopathological data of 68 BCBM patients admitted to the Air Force Medical Center, Chinese People's Liberation Army (formerly Air Force General Hospital) from 2000 to 2022 were collected. Another 136 BC patients without BM were matched at a ratio of 1:2 based on the age and site of onset for retrospective analysis. Categorical data were subjected to χ2 test or Fisher's exact probability test, and the variables with P < 0.05 in the univariate Cox proportional hazards model were incorporated into the multivariate model to identify high-risk factors and independent prognostic factors of BCBM, with a hazard ratio (HR) > 1 suggesting poor prognostic factors. The survival time of patients was estimated by the Kaplan-Meier method, and overall survival was compared between groups by log-rank test. RESULTS: Multivariate Cox regression analysis showed that patients with stage III/IV tumor at initial diagnosis [HR: 5.58, 95% confidence interval (CI): 1.99-15.68], lung metastasis (HR: 24.18, 95%CI: 6.40-91.43), human epidermal growth factor receptor 2 (HER2)-overexpressing BC and triple-negative BC were more prone to BM. As can be seen from the prognostic data, 52 of the 68 BCBM patients had died by the end of follow-up, and the median time from diagnosis of BC to the occurrence of BM and from the occurrence of BM to death or last follow-up was 33.5 and 14 mo, respectively. It was confirmed by multivariate Cox regression analysis that patients with neurological symptoms (HR: 1.923, 95%CI: 1.005-3.680), with bone metastasis (HR: 2.011, 95%CI: 1.056-3.831), and BM of HER2-overexpressing and triple-negative BC had shorter survival time. CONCLUSION: HER2-overexpressing, triple-negative BC, late tumor stage and lung metastasis are risk factors of BM. The presence of neurological symptoms, bone metastasis, and molecular type are influencing prognosis factors of BCBM.

Origin, evolution and diversification of plant mechanosensitive channel of small conductance-like (MSL) proteins.

Mechanosensitive (MS) ion channels provide efficient molecular mechanism for transducing mechanical forces into intracellular ion fluxes in all kingdoms of life. The mechanosensitive channel of small conductance (MscS) was one of the best-studied MS channels and its homologs (MSL, MscS-like) were widely distributed in cell-walled organisms. However, the origin, evolution and expansion of MSL proteins in plants are still not clear. Here, we identified more than 2100 MSL proteins from 176 plants and conducted a broad-scale phylogenetic analysis. The phylogenetic tree showed that plant MSL proteins were divided into three groups (I, II and III) prior to the emergence of chlorophytae algae, consistent with their specific subcellular localization. MSL proteins were distributed unevenly into each of plant species, and four parallel expansion was identified in angiosperms. In Brassicaceae, most MSL duplicates were derived by whole-genome duplication (WGD)/segmental duplications. Finally, a hypothetical evolutionary model of MSL proteins in plants was proposed based on phylogeny. Our studies illustrate the evolutionary history of the MSL proteins and provide a guide for future functional diversity analyses of these proteins in plants.

Peutz-Jeghers syndrome without STK11 mutation may correlate with less severe clinical manifestations in Chinese patients.

BACKGROUND: Peutz-Jeghers syndrome (PJS) is an autosomal dominant genetic disease with skin mucosal pigment spots and gastrointestinal (GI) multiple hamartoma polyps as clinical characteristics. At present, it is considered that the germline mutation of STK11 gene is the genetic cause of PJS. However, not all PJS patients can be detected STK11 germline mutations. The specific clinical characteristics of these PJS patients without STK11 mutation is an interesting clinical question. Or, like wild type GI stromal tumor, whether these PJS without STK11 mutation are also called PJS is worth discussing. Therefore, we designed the study to understand the clinical characteristics of these PJS patients without STK11 mutation. AIM: To investigates whether PJS patients with known STK11 mutations have a more severe spectrum of clinical phenotypes compared to those without. METHODS: A total of 92 patients with PJS admitted to the Air Force Medical Center from 2010 to 2022 were randomly selected for study. Genomic DNA samples were extracted from peripheral blood samples, and pathogenic germline mutations of STK11 were detected by high-throughput next-generation gene sequencing. Clinical-pathologic manifestations of patients with and without STK11/LKB1 mutations were compared. RESULTS: STK11 germline mutations were observed in 73 patients with PJS. Among 19 patients with no detectable STK11 mutations, six had no pathogenic germline mutations of other genes, while 13 had other genetic mutations. Compared with PJS patients with STK11 mutations, those without tended to be older at the age of initial treatment, age of first intussusception and age of initial surgery. They also had a lower number of total hospitalizations relating to intussusception or intestinal obstruction, and a lower load of small intestine polyps. CONCLUSION: PJS patients without STK11 mutations might have less severe clinical-pathologic manifestations than those with.

Copolymer-grafted cellulose nanocrystal induced nanocomposite hydrogels with enhanced strength, high elasticity and adhesiveness for flexible strain and pressure sensors.

Recently, the application of cellulose nanocrystals (CNCs) in the field of hydrogel sensors has attracted much attention. However, it remains challenging to construct CNC-reinforced conductive hydrogels with a combination of enhanced strength, low hysteresis, high elasticity and remarkable adhesiveness. Herein, we present a facile method to prepare conductive nanocomposite hydrogels with the above-mentioned properties by reinforcing chemically crosslinked poly(acrylic acid) (PAA) hydrogel with rational-designed copolymer-grafted CNCs. The copolymer-grafted CNCs interact with PAA matrix to form carboxyl-amide conventional hydrogen bonds and carboxyl-amino ionic hydrogen bonds, among which the ionic hydrogen bonds with rapid recovery capability are critical to the low hysteresis and high elasticity of hydrogel. The introduction of copolymer-grafted CNCs endowed the hydrogels with enhanced tensile/compressive strength, high resilience (>95 %) during tensile cyclic loading, rapid self-recovery during compressive cyclic loading and improved adhesiveness. Thanks to the high elasticity and durability of hydrogel, the assembled hydrogel sensors exhibited good cycling repeatability and durability in detecting various strains, pressures and human motions. The hydrogel sensors also showed satisfying sensitivity. Hence, the proposed preparation method and the obtained CNC-reinforced conductive hydrogels would open new avenues in flexible strain and pressure sensors for human motion detection and beyond.

Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea.

Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis), is one of the most popular nonalcoholic beverages in the world and has numerous health benefits for humans. Along with new progress in biotechnologies, the refined chromosome-scale reference tea genomes have been achieved, which facilitates great promise for the understanding of fundamental genomic architecture and evolution of the tea plants. Here, we summarize recent achievements in genome sequencing in tea plants and review the new progress in origin and evolution of tea plants by population sequencing analysis. Understanding the genomic characterization of tea plants is import to improve tea quality and accelerate breeding in tea plants.

Peptide signaling in anther development and pollen-stigma interactions.

Polypeptides play irreplaceable roles in cell-cell communication by binding to receptor-like kinases. Various types of peptide-receptor-like kinase-mediated signaling have been identified in anther development and male-female interactions in flowering plants. Here, we provide a comprehensive summary of the biological functions and signaling pathways of peptides and receptors involved in anther development, self-incompatibility, pollen tube growth and pollen tube guidance.

The lineage-specific evolution of the oleosin family in Theaceae.

Oleosins play essential roles in stabilization of lipid droplets (LDs) and seed oil production. However, evolution of this gene family has not been reported in Theaceae, a large plant family that contains many important tea and oil tea species. In this study, a total of 65 oleosin genes were identified in nine genome-sequenced Theaceae species. Among these genomes, the gene number of oleosin showed significant difference, with Camellia sinensis var. sinensis cv. Shuchazao and Camellia lanceoleosa displayed more oleosin numbers than other species. Phylogenetic analyses revealed that Theaceae oleosin genes were classified into three clades (U, SL, SH) respectively. Proteins within the same clade had similar gene structure and motif composition. Segmental duplication was the primary driving force for the evolution of oleosin genes in Shuchazao (SCZ), Huangdan (HD), C.lanceoleosa (Cla), and wild tea (DASZ). Synteny analysis showed that most oleosin genes displayed inter-species synteny among tea and oil tea species. Expression analysis demonstrated that oleosin genes were specifically expressed in seed and kernel of Huangdan (HD) and C.lanceoleosa. Moreover, expression divergence was observed in paralogous pairs and ∼1-2 oleosin genes in each clade have become activate. This study leads to a comprehensive understanding of evolution of oleosin family in Theaceae, and provides a rich resource to further address the functions of oleosin in tea and oil tea species.

Clinical features, diagnosis, and treatment of Peutz-Jeghers syndrome: Experience with 566 Chinese cases.

BACKGROUND: Peutz-Jeghers syndrome (PJS) is a clinically rare disease with pigmented spots on the lips and mucous membranes and extremities, scattered gastrointestinal polyps, and susceptibility to tumors as clinical manifestations. Effective preventive and curative methods are still lacking. Here we summarize our experience with 566 Chinese patients with PJS from a Chinese medical center with regard to the clinical features, diagnosis, and treatment. AIM: To explore the clinical features, diagnosis, and treatment of PJS in a Chinese medical center. METHODS: The diagnosis and treatment information of 566 cases of PJS admitted to the Air Force Medical Center from January 1994 to October 2022 was summarized. A clinical database was established covering age, gender, ethnicity, family history, age at first treatment, time and sequence of appearance of mucocutaneous pigmentation, polyp distribution, quantity, and diameter, frequency of hospitalization, frequency of surgical operations, etc. The clinical data was retrospectively analyzed using SPSS 26.0 software, with P < 0.05 considered statistically significant. RESULTS: Of all the patients included, 55.3% were male and 44.7% were female. Median time to the appearance of mucocutaneous pigmentation was 2 years, and median time from the appearance of mucocutaneous pigmentation to the occurrence of abdominal symptoms was 10 years. The vast majority (92.2%) of patients underwent small bowel endoscopy and treatment, with 2.3% having serious complications. There was a statistically significant difference in the number of enteroscopies between patients with and without canceration (P = 0.004, Z = -2.882); 71.2% of patients underwent surgical operation, 75.6% of patients underwent surgical operation before the age of 35 years, and there was a statistically significant difference in the frequency of surgical operations between patients with and without cancer (P = 0.000, Z = -5.127). At 40 years of age, the cumulative risk of intussusception in PJS was approximately 72.0%, and at 50 years, the cumulative risk of intussusception in PJS was approximately 89.6%. At 50 years of age, the cumulative risk of cancer in PJS was approximately 49.3%, and at 60 years of age, the cumulative risk of cancer in PJS was approximately 71.7%. CONCLUSION: The risk of intussusception and cancer of PJS polyps increases with age. PJS patients ≥ 10 years old should undergo annual enteroscopy. Endoscopic treatment has a good safety profile and can reduce the occurrence of polyps intussusception and cancer. Surgery should be conducted to protect the gastrointestinal system by removing polyps.

How much can deep learning improve prediction of the responses to drugs in cancer cell lines?

The drug response prediction problem arises from personalized medicine and drug discovery. Deep neural networks have been applied to the multi-omics data being available for over 1000 cancer cell lines and tissues for better drug response prediction. We summarize and examine state-of-the-art deep learning methods that have been published recently. Although significant progresses have been made in deep learning approach in drug response prediction, deep learning methods show their weakness for predicting the response of a drug that does not appear in the training dataset. In particular, all the five evaluated deep learning methods performed worst than the similarity-regularized matrix factorization (SRMF) method in our drug blind test. We outline the challenges in applying deep learning approach to drug response prediction and suggest unique opportunities for deep learning integrated with established bioinformatics analyses to overcome some of these challenges.

Path-folded infrared spectrometer consisting of 10 sub-gratings and a two-dimensional InGaAs detector.

A new compact infrared spectrometer without any mechanical moving elements has been designed and constructed using a two-dimensional InGaAs array detector and 10 sub-gratings. The instrument is compact, with a double-folded optical path configuration. The spectra are densely 10-folded to achieve 0.07-nm spectral resolution and a 2-ms data acquisition time in the 1450- to 1650-nm wavelength region, making the instrument useful for real-time spectroscopic data analyses in optical communication and many other fields.