The monthly remodeling, shedding, and regeneration of the endometrium defining the human menstrual cycle is driven by gene expression changes in the underlying tissue hierarchy. Significant heterogeneity exists among cell types in the endometrium, such that multiple cell types vary dramatically in state through a monthly cycle and undergo various forms of differentiation at rapid rates. Histologic analysis and whole-tissue transcriptomic profiling have defined a specific molecular state as the optimal timing of the window of implantation (WOI) for in vitro fertilization transfer.This single-cell transcriptomic analysis aimed to characterize the transcriptomic transformation of human endometrium at single-cell resolution across the menstrual cycle, including at the WOI. Endometrial biopsies were collected from 19 healthy ovum donors between 4 and 27 days following menses, and single cells were captured and complementary DNA was generated using Fluidigm C1 medium chips. Six cell types were identified across the menstrual cycle: stromal fibroblast, endothelium, macrophage, lymphocyte, ciliated epithelium, and unciliated epithelium.Endometrial transformation was analyzed by within-cell type t-SNE using whole-transcriptome data from unciliated epithelia and stromal fibroblasts, the 2 major contributing cell types to endometrial transformation. This revealed 4 major, time-associated phases of both cell types. Among unciliated epithelia, single-cell gene dynamics were relatively continuous across phases 1 to 3 until an abrupt activation of genes consistently reported in whole-tissue transcriptomic data sets as overexpressed in the WOI marked entrance into phase 4. Among stromal fibroblasts, the WOI was characterized by widespread decidualization that became gradually upregulated through phase progression. Likewise, the WOI closed with more gradual transition dynamics in both cell types.The traditional definition of endometrial phases, consisting of the proliferative and secretory phases, correlated with the 4 phases identified here through single-cell analysis. Cell-cycling was elevated in phases 1 and 2 and ceased in later phases, suggesting the transition from proliferative to secretory occurred between phase 2 and 3. At the transcriptomic level, proliferative endometrium can be divided into 2 distinct phases with unique transcriptomic signatures.This study involved the systematic characterization of the human endometrium across the menstrual cycle through dynamic gene expression mapping. The results demonstrate that ciliated epithelium are a transcriptomically distinct endometrial cell type that are highly prevalent in the human endometrium and constantly changing in abundance across the cycle. This study likewise demonstrated an abrupt and strong transcriptomic activation in unciliated epithelia and a gradual activation in stromal fibroblasts to define the opening of the WOI, indicating a potential diagnostic target for more precise in vitro fertilization and embryo transfer.

Significance Circulating cell-free RNA in the blood provides a potential window into the health, phenotype, and developmental programs of a variety of human organs. We used high-throughput methods of RNA analysis such as microarrays and next-generation sequencing to characterize the global landscape of circulating RNA in human subjects. By focusing on tissue-specific genes, we were able to identify the relative contributions of these tissues to circulating RNA and monitor changes during tissue development and neurodegenerative disease states.

Noninvasive blood tests that provide information about fetal development and gestational age could potentially improve prenatal care. Ultrasound, the current gold standard, is not always affordable in low-resource settings and does not predict spontaneous preterm birth, a leading cause of infant death. In a pilot study of 31 healthy pregnant women, we found that measurement of nine cell-free RNA (cfRNA) transcripts in maternal blood predicted gestational age with comparable accuracy to ultrasound but at substantially lower cost. In a related study of 38 women (23 full-term and 15 preterm deliveries), all at elevated risk of delivering preterm, we identified seven cfRNA transcripts that accurately classified women who delivered preterm up to 2 months in advance of labor. These tests hold promise for prenatal care in both the developed and developing worlds, although they require validation in larger, blinded clinical trials.

BACKGROUND Detecting tumor-derived cell-free DNA (cfDNA) in the blood of brain tumor patients is challenging, presumably owing to the blood–brain barrier. Cerebral spinal fluid (CSF) may serve as an alternative “liquid biopsy” of brain tumors by enabling measurement of circulating DNA within CSF to characterize tumor-specific mutations. Many aspects about the characteristics and detectability of tumor mutations in CSF remain undetermined. METHODS We used digital PCR and targeted amplicon sequencing to quantify tumor mutations in the cfDNA of CSF and plasma collected from 7 patients with solid brain tumors. Also, we applied cancer panel sequencing to globally characterize the somatic mutation profile from the CSF of 1 patient with suspected leptomeningeal disease. RESULTS We detected tumor mutations in CSF samples from 6 of 7 patients with solid brain tumors. The concentration of the tumor mutant alleles varied widely between patients, from <5 to nearly 3000 copies/mL CSF. We identified 7 somatic mutations from the CSF of a patient with leptomeningeal disease by use of cancer panel sequencing, and the result was concordant with genetic testing on the primary tumor biopsy. CONCLUSIONS Tumor mutations were detectable in cfDNA from the CSF of patients with different primary and metastatic brain tumors. We designed 2 strategies to characterize tumor mutations in CSF for potential clinical diagnosis: the targeted detection of known driver mutations to monitor brain metastasis and the global characterization of genomic aberrations to direct personalized cancer care.

Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated.

Cell-free RNA (cfRNA) is a promising analyte for cancer detection. However, a comprehensive assessment of cfRNA in individuals with and without cancer has not been conducted. We perform the first transcriptome-wide characterization of cfRNA in cancer (stage III breast [n = 46], lung [n = 30]) and non-cancer (n = 89) participants from the Circulating Cell-free Genome Atlas (NCT02889978). Of 57,820 annotated genes, 39,564 (68%) are not detected in cfRNA from non-cancer individuals. Within these low-noise regions, we identify tissue- and cancer-specific genes, defined as “dark channel biomarker” (DCB) genes, that are recurrently detected in individuals with cancer. DCB levels in plasma correlate with tumor shedding rate and RNA expression in matched tissue, suggesting that DCBs with high expression in tumor tissue could enhance cancer detection in patients with low levels of circulating tumor DNA. Overall, cfRNA provides a unique opportunity to detect cancer, predict the tumor tissue of origin, and determine the cancer subtype.

Single crystalline h-MoO 3 nano-and microrods were successfully synthesized using modified liquid-phase processes with concentrated HNO 3 and H 2 SO 4 . Their X-ray powder diffraction (XRD) data were unambiguously indexed based on a hexagonal structure with the lattice constants a ≈ 10.57 and c ≈ 3.72 A ˚instead of a = 10.53 and c = 14.98 A ˚(JCPDS 21-0569) usually adopted. Rietveld refinements of the XRD data were pioneeringly performed based on the (Na 3 2H 2 O)Mo 5.33 -[H 4.5 ] 0.67 O 18 structure with the space group of P6 3 /m regardless of H þ and Na þ . Nanorods synthesized under different conditions show different sizes and aspect ratios. Annealing at 300 °C for 3 h significantly improves the crystallinity and phase purity of as-synthesized h-MoO 3 rods, which is evidenced by sharpening of peaks in micro-Raman spectra with no shift. An irreversible transition from h-MoO 3 to R-MoO 3 occurring between 413 and 436 °C can be triggered by irradiation of either electrons or laser with high energies or powers as well. The turning points on both differential thermal analysis (DTA) and thermogravimetry (TG) curves show presence of water molecules interacted differently with the lattice which escape at different temperatures. h-MoO 3 rods reduce the temperatures of soot oxidation to 482-490 °C, much higher than its structural transition temperatures. This makes it simply suitable for catalyzing reactions taking place at temperatures lower than the transition temperatures, say, as the catalyst of the selective oxidation of methanol.

We develop a novel method for Western blot based on microfluidics, incorporating the internal molecular weight marker, loading control, and antibody titration in the same protocol. Compared with the conventional method which could detect only one protein, the microfluidic Western blot could analyze at least 10 proteins simultaneously from a single sample, and it requires only about 1% of the amount of antibody used in conventional Western blot.