Frequent disturbances enhanced the resilience of past human populations.

The record of past human adaptations provides crucial lessons for guiding responses to crises in the future1-3. To date, there have been no systematic global comparisons of humans' ability to absorb and recover from disturbances through time4,5. Here we synthesized resilience across a broad sample of prehistoric population time-frequency data, spanning 30,000 years of human history. Cross-sectional and longitudinal analyses of population decline show that frequent disturbances enhance a population's capacity to resist and recover from later downturns. Land-use patterns are important mediators of the strength of this positive association: farming and herding societies are more vulnerable but also more resilient overall. The results show that important trade-offs exist when adopting new or alternative land-use strategies.

Comparison of calibration strategies for accurate quantitation by isotope dilution mass spectrometry: a case study of ochratoxin A in flour.

Analysis of low-level organic contaminants in complex matrices is essential for monitoring global food safety. However, balancing sample throughput with complex experimental designs and/or sample clean-up to best reduce matrix effects is a constant challenge. Multiple strategies exist to mitigate these effects, with internal standard-based methods such as isotope dilution mass spectrometry (IDMS) being the most advantageous. Here, multiple internal calibration strategies were investigated for the quantification of ochratoxin A (OTA) in wheat samples by liquid chromatography-mass spectrometry (LC-MS). Internal standard-based quantitation methods such as single (ID1MS), double (ID2MS), and quintuple (ID5MS) isotope dilution mass spectrometry, as well as external standard calibration, were explored and compared. A certified reference material (CRM) of OTA in flour, MYCO-1, was used to evaluate the accuracy of each method. External calibration generated results 18-38% lower than the certified value for MYCO-1, largely due to matrix suppression effects. Concurrently, consistently lower OTA mass fractions were obtained for the wheat samples upon quantitation by external calibration as opposed to ID1MS, ID2MS, and ID5MS. All isotope dilution methods produced results that fell within the expected range for MYCO-1 (3.17-4.93 µg/kg), validating their accuracy. However, an average 6% decrease in the OTA mass fraction was observed from results obtained by ID1MS compared to those by ID2MS and ID5MS. Upon scrutiny, these differences were attributed to an isotopic enrichment bias in the isotopically labelled internal standard [13C6]-OTA that was used for ID1MS, the OTAL-1 CRM. The advantages and limitations of each isotopic method are illustrated.

Cold Ethanol Extraction of Cannabinoids and Terpenes from Cannabis Using Response Surface Methodology: Optimization and Comparative Study.

Efficient cannabis biomass extraction can increase yield while reducing costs and minimizing waste. Cold ethanol extraction was evaluated to maximize yield and concentrations of cannabinoids and terpenes at different temperatures. Central composite rotatable design was used to optimize two independent factors: sample-to-solvent ratio (1:2.9 to 1:17.1) and extraction time (5.7 min-34.1 min). With response surface methodology, predicted optimal conditions at different extraction temperatures were a cannabis-to-ethanol ratio of 1:15 and a 10 min extraction time. With these conditions, yields (g 100 g dry matter-1) were 18.2, 19.7, and 18.5 for -20 °C, -40 °C and room temperature, respectively. Compared to the reference ground sample, tetrahydrocannabinolic acid changed from 17.9 (g 100 g dry matter-1) to 15, 17.5, and 18.3 with an extraction efficiency of 83.6%, 97.7%, 102.1% for -20 °C, -40 °C, and room temperature, respectively. Terpene content decreased by 54.1% and 32.2% for extraction at -20 °C and room temperature, respectively, compared to extraction at -40 °C. Principal component analysis showed that principal component 1 and principal component 2 account for 88% and 7.31% of total variance, respectively, although no significant differences in cold ethanol extraction at different temperatures were observed.

Microwave- and Ultrasound-Assisted Extraction of Cannabinoids and Terpenes from Cannabis Using Response Surface Methodology.

Limited studies have explored different extraction techniques that improve cannabis extraction with scale-up potential. Ultrasound-assisted and microwave-assisted extraction were evaluated to maximize the yield and concentration of cannabinoids and terpenes. A central composite rotatable design was used to optimize independent factors (sample-to-solvent ratio, extraction time, extraction temperature, and duty cycle). The optimal conditions for ultrasound- and microwave-assisted extraction were the sample-to-solvent ratios of 1:15 and 1:14.4, respectively, for 30 min at 60 °C. Ultrasound-assisted extraction yielded 14.4% and 14.2% more oil and terpenes, respectively, compared with microwave-assisted extracts. Ultrasound-assisted extraction increased cannabinoid concentration from 13.2−39.2%. Considering reference ground samples, tetrahydrocannabinolic acid increased from 17.9 (g 100 g dry matter−1) to 28.5 and 20 with extraction efficiencies of 159.2% and 111.4% for ultrasound-assisted and microwave-assisted extraction, respectively. Principal component analyses indicate that the first two principal components accounted for 96.6% of the total variance (PC1 = 93.2% and PC2 = 3.4%) for ultrasound-assisted extraction and 92.4% of the total variance (PC1 = 85.4% and PC2 = 7%) for microwave-assisted extraction. Sample-to-solvent ratios significantly (p < 0.05) influenced the secondary metabolite profiles and yields for ultrasound-assisted extracts, but not microwave-assisted extracts.

Microbiota promote secretory cell determination in the intestinal epithelium by modulating host Notch signaling.

Resident microbes promote many aspects of host development, although the mechanisms by which microbiota influence host tissues remain unclear. We showed previously that the microbiota is required for allocation of appropriate numbers of secretory cells in the zebrafish intestinal epithelium. Because Notch signaling is crucial for secretory fate determination, we conducted epistasis experiments to establish whether the microbiota modulates host Notch signaling. We also investigated whether innate immune signaling transduces microbiota cues via the Myd88 adaptor protein. We provide the first evidence that microbiota-induced, Myd88-dependent signaling inhibits host Notch signaling in the intestinal epithelium, thereby promoting secretory cell fate determination. These results connect microbiota activity via innate immune signaling to the Notch pathway, which also plays crucial roles in intestinal homeostasis throughout life and when impaired can result in chronic inflammation and cancer.

Long-read nanopore sequencing resolves a TMEM231 gene conversion event causing Meckel-Gruber syndrome.

The diagnostic deployment of massively parallel short-read next-generation sequencing (NGS) has greatly improved genetic test availability, speed, and diagnostic yield, particularly for rare inherited disorders. Nonetheless, diagnostic approaches based on short-read sequencing have a poor ability to accurately detect gene conversion events. We report on the genetic analysis of a family in which 3 fetuses had clinical features consistent with the autosomal recessive disorder Meckel-Gruber syndrome (MKS). Targeted NGS of 29 known MKS-associated genes revealed a heterozygous TMEM231 splice donor variant c.929+1A>G. Comparative read-depth analysis, performed to identify a second pathogenic allele, revealed an apparent heterozygous deletion of TMEM231 exon 4. To verify this result we performed single-molecule long-read sequencing of a long-range polymerase chain reaction product spanning this locus. We identified four missense variants that were absent from the short-read dataset due to the preferential mapping of variant-containing reads to a downstream TMEM231 pseudogene. Consistent with the parental segregation analysis, we demonstrate that the single-molecule long reads could be used to show that the variants are arranged in trans. Our experience shows that robust validation of apparent dosage variants remains essential to avoid the pitfalls of short-read sequencing and that new third-generation long-read sequencing technologies can already aid routine clinical care.

Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications.

The widespread use of genome-wide diagnostic screening methods has greatly increased the frequency with which incidental (but possibly pathogenic) copy number changes affecting single genes are detected. These findings require validation to allow appropriate clinical management. Deletion variants can usually be readily validated using a range of short-read next-generation sequencing (NGS) strategies, but the characterization of duplication variants at nucleotide resolution remains challenging. This presents diagnostic problems, since pathogenicity cannot generally be assessed without knowing the structure of the variant. We have used a novel Cas9 enrichment strategy, in combination with long-read single-molecule nanopore sequencing, to address this need. We describe the nucleotide-level resolution of two problematic cases, both of whom presented with neurodevelopmental problems and were initially investigated by array CGH. In the first case, an incidental 1.7-kb imbalance involving a partial duplication of VHL exon 3 was detected. This variant was inherited from the patient's father, who had a history of renal cancer at 38 years. In the second case, an incidental ~200-kb de novo duplication that included DMD exons 30-44 was resolved. In both cases, the long-read data yielded sufficient information to enable Sanger sequencing to define the rearrangement breakpoints, and creation of breakpoint-spanning PCR assays suitable for testing of relatives. Our Cas9 enrichment and nanopore sequencing approach can be readily adopted by molecular diagnostic laboratories for cost-effective and rapid characterization of challenging duplication-containing alleles. We also anticipate that in future this method may prove useful for characterizing acquired translocations in tumor cells, and for precisely identifying transgene integration sites in mouse models.

Dendritic cells in IBD pathogenesis: an area of therapeutic opportunity?

Dysfunction of the mucosal immune system plays an important role in inflammatory bowel disease (IBD) pathogenesis. Dendritic cells are emerging as central players based on both our increasing understanding of how genetic susceptibility impacts the mucosal immune system and the key role of dendritic cells in regulating response to gut microflora. We discuss areas of therapeutic opportunity in this evolving landscape.

Opioid-sparing Anesthesia Decreases In-hospital and 1-year Postoperative Opioid Consumption Compared With Traditional Anesthesia: A Propensity-matched Cohort Study.

STUDY DESIGN: Propensity-matched cohort. OBJECTIVE: The aim of this study was to determine if opioid-sparing anesthesia (OSA) reduces in-hospital and 1-year postoperative opioid consumption. SUMMARY OF BACKGROUND DATA: The recent opioid crisis highlights the need to reduce opioid exposure. We developed an OSA protocol for lumbar spinal fusion surgery to mitigate opioid exposure. MATERIALS AND METHODS: Patients undergoing lumbar fusion for degenerative conditions over one to four levels were identified. Patients taking opioids preoperatively were excluded. OSA patients were propensity-matched to non-OSA patients based on age, sex, smoking status, body mass index, American Society of Anesthesiologists grade, and revision versus primary procedure. Standard demographic and surgical data, daily in-hospital opioid consumption, and opioid prescriptions 1 year after surgery were compared. RESULTS: Of 296 OSA patients meeting inclusion criteria, 172 were propensity-matched to non-OSA patients. Demographics were similar between cohorts (OSA: 77 males, mean age=57.69 yr; non-OSA: 67 males, mean age=58.94 yr). OSA patients had lower blood loss (326 mL vs. 399 mL, P =0.014), surgical time (201 vs. 233 min, P <0.001) emergence to extubation time (9.1 vs. 14.2 min, P< 0.001), and recovery room time (119 vs. 140 min, P =0.0.012) compared with non-OSA patients. Fewer OSA patients required nonhome discharge (18 vs. 41, P =0.001) compared with the non-OSA cohort, but no difference in length of stay (90.3 vs. 98.5 h, P =0.204). Daily opioid consumption was lower in the OSA versus the non-OSA cohort from postoperative day 2 (223 vs. 185 morphine milligram equivalents, P =0.017) and maintained each day with lower total consumption (293 vs. 225 morphine milligram equivalents, P =0.003) throughout postoperative day 4. The number of patients with active opioid prescriptions at 1, 3, 6, and 12 months postoperative was statistically fewer in the OSA compared with the non-OSA patients. CONCLUSIONS: OSA for lumbar spinal fusion surgery decreases in-hospital and 1-year postoperative opioid consumption. The minimal use of opioids may also lead to shorter emergence to extubation times, shorter recovery room stays, and fewer discharges to nonhome facilities.

Expression of phosphorylated signal transducer and activator of transcription 5 is associated with an increased risk of death in acute myeloid leukemia.

BACKGROUND: Constitutive activation of STAT5 (by phosphorylation) has been identified in a number of malignancies, including acute myeloid leukemia (AML). OBJECTIVES: We investigated whether the level of phosphorylated STAT5 (pSTAT5) expression correlates with clinical outcome in AML. METHODS: Adult patients with newly diagnosed AML receiving induction chemotherapy and with an available diagnostic bone marrow were evaluated. RESULTS: Forty-two percent of patients had pSTAT5 expression >0 on immunohistochemical analysis of fixed bone marrow core biopsies. In multivariable analyses, controlling for age, history of antecedent hematologic disorder, cytogenetic risk, and WBC at diagnosis, pSTAT5 expression was significantly associated with an increased risk of death (HR 1.96, 95% CI 1.19-3.23, P = 0.008) and of relapse after achieving complete remission (HR 2.31, 95% CI 1.16-4.63, P = 0.018). CONCLUSIONS: Validation of pSTAT5's prognostic value requires additional study in a larger group of uniformly treated patients. However, our data suggests that targeting this signaling pathway in AML may improve the outcome of patients.

Absolute lymphocyte count at day 28 independently predicts event-free and overall survival in adults with newly diagnosed acute lymphoblastic leukemia.

We investigated the prognostic impact of absolute lymphocyte count (ALC) following induction chemotherapy in newly diagnosed adult acute lymphoblastic leukemia (ALL). Patients with ALC ≥350 cells/µL at day 28 had a median overall survival (OS) of 47.4 months when compared with 17.6 months for those with an ALC <350 cells/µL (HR = 1.98, P = 0.007). Among patients who achieved a complete remission, median event-free survival (EFS) for those with ALC ≥350 cells/µL on day 28 was 42.1 months when compared with 13.9 months in those with ALC <350 cells/µL (HR = 2.08, P = 0.006). In multivariable analysis, the ALC on day 28 (<350 cells/µL vs. ≥350 cells/µL, P ≤ .0004 for OS and EFS) along with WBC at diagnosis (≤6.0 or >30.0 K/µL vs. >6.0-30.0 K/µL, P ≤ 0.002 for OS and EFS) and cytogenetics (abnormal vs. normal, P = 0.002 for OS and P = 0.02 for EFS) were independent prognostic factors of both OS and EFS. Combining these three factors segregates patients in three well-defined risk groups. These data suggest that ALC can be used in combination with other prognostic features to better predict outcome and that targeting the immune system to improve ALC may be a worthwhile strategy in ALL.

Tautomerization and Isomerization in Quantitative NMR: A Case Study with 4-Deoxynivalenol (DON).

The regulated mycotoxin 4-deoxynivalenol (DON) has a heterocyclic structure that is readily amenable to tautomerization and conformational isomerization in solution. An analysis of DON in solution by NMR revealed the presence of hemiacetal tautomer(s) and putative conformational isomers, which maintain the intact enone functional group. The extent and type of tautomerization/isomerization vary according to the NMR solvent used and produce different signal patterns in the NMR spectra. Thus, the same proton produces multiple signals depending on which isomer/tautomer it belongs to. To maintain the accuracy of quantitative NMR (qNMR) measurements, it was essential to conclusively identify all signals belonging to the same proton to avoid underestimating its integral value. A strategy to overcome the complications of DON tautomerization and isomerization in solution during qNMR is reported. Of all proton atoms on the DON carbo-skeleton, H-10 produced clearly defined signals centered at 6.6 ppm for suspected conformational isomers and at 5.5 ppm for hemiacetal tautomers. To determine the purity of DON by quantitative proton NMR, the collective integrals of all isomeric and tautomeric signals belonging to H-10 provided the most accurate value. The purity of DON obtained with this protocol is highly accurate and suitable for the value assignment of certified reference materials (CRMs).

Mapping past human land use using archaeological data: A new classification for global land use synthesis and data harmonization.

In the 12,000 years preceding the Industrial Revolution, human activities led to significant changes in land cover, plant and animal distributions, surface hydrology, and biochemical cycles. Earth system models suggest that this anthropogenic land cover change influenced regional and global climate. However, the representation of past land use in earth system models is currently oversimplified. As a result, there are large uncertainties in the current understanding of the past and current state of the earth system. In order to improve representation of the variety and scale of impacts that past land use had on the earth system, a global effort is underway to aggregate and synthesize archaeological and historical evidence of land use systems. Here we present a simple, hierarchical classification of land use systems designed to be used with archaeological and historical data at a global scale and a schema of codes that identify land use practices common to a range of systems, both implemented in a geospatial database. The classification scheme and database resulted from an extensive process of consultation with researchers worldwide. Our scheme is designed to deliver consistent, empirically robust data for the improvement of land use models, while simultaneously allowing for a comparative, detailed mapping of land use relevant to the needs of historical scholars. To illustrate the benefits of the classification scheme and methods for mapping historical land use, we apply it to Mesopotamia and Arabia at 6 kya (c. 4000 BCE). The scheme will be used to describe land use by the Past Global Changes (PAGES) LandCover6k working group, an international project comprised of archaeologists, historians, geographers, paleoecologists, and modelers. Beyond this, the scheme has a wide utility for creating a common language between research and policy communities, linking archaeologists with climate modelers, biodiversity conservation workers and initiatives.

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt.

Intestinal stem cells are non-quiescent, dividing epithelial cells that rapidly differentiate into progenitor cells of the absorptive and secretory cell lineages. The kinetics of this process is rapid such that the epithelium is replaced weekly. To determine how the transcriptome and proteome keep pace with rapid differentiation, we developed a new cell sorting method to purify mouse colon epithelial cells. Here we show that alternative mRNA splicing and polyadenylation dominate changes in the transcriptome as stem cells differentiate into progenitors. In contrast, as progenitors differentiate into mature cell types, changes in mRNA levels dominate the transcriptome. RNA processing targets regulators of cell cycle, RNA, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.

Publisher Correction: Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Certification of Ochratoxin A Reference Materials: Calibration Solutions OTAN-1 and OTAL-1 and a Mycotoxin-Contaminated Rye Flour MYCO-1.

Background: Among the regulated mycotoxins that contaminate global food supplies, ochratoxin A is particularly harmful as a nephrotoxin and suspected carcinogen. Objective: To support global measurement comparability, certified calibration solutions for ochratoxin A and [13C6]-ochratoxin A (OTAN-1 and OTAL-1, respectively) as well as a mycotoxin-contaminated rye flour certified reference material (CRM) known as MYCO-1 were developed. Methods: Quantitative proton NMR was used along with maleic acid as an external standard traceable to the Système international (SI) to measure the concentration of ochratoxin A and [13C6]-ochratoxin A for the calibration solutions. OTAN-1 and OTAL-1 were then used as a pair in double isotope dilution MS to certify the mass fraction of ochratoxin A in MYCO-1. The natural ochratoxin A CRM served as the primary standard for traceable quantitation, while the synthetic [13C6]-ochratoxin A CRM served as the internal standard. Results: The certified mass fraction of ochratoxin A or [13C6]-ochratoxin A in the two mycotoxin calibration solution standards was established to be 11.03 ± 0.32 µg/g (k = 2) for OTAN-1 and 4.89 ± 0.18 µg/g (k = 2) for OTAL-1. The mass fraction of ochratoxin A in the rye flour standard MYCO-1 was certified at 4.05 ± 0.88 µg/kg (k = 2). Conclusions: These CRMs will support regulatory testing as they can be used in the method development, validation, calibration, and QC analysis of ochratoxin A. Highlights: This report highlights the methods used to certify OTAN-1, OTAL-1, and MYCO-1 as well as the challenges associated with producing such materials, which can be applied to a wide variety of other CRMs.

Imaging of Activated T Cells as an Early Predictor of Immune Response to Anti-PD-1 Therapy.

Compelling evidence points to immune cell infiltration as a critical component of successful immunotherapy. However, there are currently no clinically available, noninvasive methods capable of evaluating immune contexture prior to or during immunotherapy. In this study, we evaluate a T-cell-specific PET agent, [18F]F-AraG, as an imaging biomarker predictive of response to checkpoint inhibitor therapy. We determined the specificity of the tracer for activated T cells in vitro and in a virally induced model of rhabdomyosarcoma. Of all immune cells tested, activated human CD8+ effector cells showed the highest accumulation of [18F]F-AraG. Isolation of lymphocytes from the rhabdomyosarcoma tumors showed that more than 80% of the intratumoral signal came from accumulation of [18F]F-AraG in immune cells, primarily CD8+ and CD4+. Longitudinal monitoring of MC38 tumor-bearing mice undergoing anti-PD-1 treatment revealed differences in signal between PD-1 and isotype antibody-treated mice early into treatment. The differences in [18F]F-AraG signal were also apparent between responders and nonresponders to anti-PD-1 therapy. Importantly, we found that the signal in the tumor-draining lymph nodes provides key information about response to anti-PD-1 therapy. Overall, [18F]F-AraG has potential to serve as a much needed immunomonitoring clinical tool for timely evaluation of immunotherapy. SIGNIFICANCE: These findings reveal differences in T-cell activation between responders and nonresponders early into anti-PD-1 treatment, which may impact many facets of immuno-oncology, including patient selection, management, and development of novel combinatorial approaches.

Correction: Journey to the east: Diverse routes and variable flowering times for wheat and barley en route to prehistoric China.

[This corrects the article DOI: 10.1371/journal.pone.0187405.].

Exploring Indus crop processing: combining phytolith and macrobotanical analyses to consider the organisation of agriculture in northwest India c. 3200-1500 bc.

This paper presents a preliminary study combining macrobotanical and phytolith analyses to explore crop processing at archaeological sites in Haryana and Rajasthan, northwest India. Current understanding of the agricultural strategies in use by populations associated with South Asia's Indus Civilisation (3200-1900 bc) has been derived from a small number of systematic macrobotanical studies focusing on a small number of sites, with little use of multi-proxy analysis. In this study both phytolith and macrobotanical analyses are used to explore the organisation of crop processing at five small Indus settlements with a view to understanding the impact of urban development and decline on village agriculture. The differing preservation potential of the two proxies has allowed for greater insights into the different stages of processing represented at these sites: with macrobotanical remains allowing for more species-level specific analysis, though due to poor chaff presentation the early stages of processing were missed; however these early stages of processing were evident in the less highly resolved but better preserved phytolith remains. The combined analyses suggests that crop processing aims and organisation differed according to the season of cereal growth, contrary to current models of Indus Civilisation labour organisation that suggest change over time. The study shows that the agricultural strategies of these frequently overlooked smaller sites question the simplistic models that have traditionally been assumed for the time period, and that both multi-proxy analysis and rural settlements are deserving of further exploration.

Caveolin1 Is Required for Th1 Cell Infiltration, but Not Tight Junction Remodeling, at the Blood-Brain Barrier in Autoimmune Neuroinflammation.

Lymphocytes cross vascular boundaries via either disrupted tight junctions (TJs) or caveolae to induce tissue inflammation. In the CNS, Th17 lymphocytes cross the blood-brain barrier (BBB) before Th1 cells; yet this differential crossing is poorly understood. We have used intravital two-photon imaging of the spinal cord in wild-type and caveolae-deficient mice with fluorescently labeled endothelial tight junctions to determine how tight junction remodeling and caveolae regulate CNS entry of lymphocytes during the experimental autoimmune encephalomyelitis (EAE) model for multiple sclerosis. We find that dynamic tight junction remodeling occurs early in EAE but does not depend upon caveolar transport. Moreover, Th1, but not Th17, lymphocytes are significantly reduced in the inflamed CNS of mice lacking caveolae. Therefore, tight junction remodeling facilitates Th17 migration across the BBB, whereas caveolae promote Th1 entry into the CNS. Moreover, therapies that target both tight junction degradation and caveolar transcytosis may limit lymphocyte infiltration during inflammation.