Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue.

Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and certain oral and intestinal pathogens have been associated with cancer development and progression. We asked if esophageal microbiomes had shared alterations that could provide novel biomarkers for ESCA risk. We extracted DNA from tumor and non-tumor tissue of 212 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNA-seq (n = 172) and WGS (n = 123) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alterations that allow disease progression in esophageal cancer.

Epigenetic processes in plant stress priming: Open questions and new approaches.

Priming reflects the capacity of plants to memorise environmental stress experience and improve their response to recurring stress. Epigenetic modifications in DNA and associated histone proteins may carry short-term and long-term memory in the same plant or mediate transgenerational effects, but the evidence is still largely circumstantial. New experimental tools now enable scientists to perform targeted manipulations that either prevent or generate a particular epigenetic modification in a particular location of the genome. Such 'reverse epigenetics' approaches allow for the interrogation of causality between individual priming-induced modifications and their role for altering gene expression and plant performance under recurring stress. Furthermore, combining site-directed epigenetic manipulation with conditional and cell-type specific promoters creates novel opportunities to test and engineer spatiotemporal patterns of priming.

The effectiveness and safety of heat/cold therapy in adults with lymphoedema: systematic review.

PURPOSE: The aim of this review is to assess the efficacy and safety of using heat and cold therapy for adults with lymphoedema. METHODS: A multi-database search was undertaken. Only studies which included adults with lymphoedema who were treated with heat or cold therapy reporting any outcome were included. Screening, data extraction, and assessment of bias were undertaken by a single reviewer and verified by a second. Due to the substantial heterogeneity, a descriptive synthesis was undertaken. RESULTS: Eighteen studies were included. All nine studies which assessed the effects of heat-therapy on changes in limb circumference reported a point estimate indicating some reduction from baseline to end of study. Similarly, the five studies evaluating the use of heat-therapy on limb volume demonstrated a reduction in limb volume from baseline to end-of-study. Only four studies reported adverse events of which all were deemed to be minor. Only two studies explored the effects of cold therapy on lymphoedema. CONCLUSIONS: Tentative evidence suggests heat-therapy may have some benefit in treating lymphoedema with minimal side effects. However, further high-quality randomised controlled trials are required, with a particular focus on moderating factors and assessment of adverse events.Implications for rehabilitationThis review highlights the potential benefit that heat therapy may have on reducing limb circumference and volume for adults with lymphoedema.There was no evidence that controlled localised heat therapy was unsafe.The current evidence-base is at a point where no specific clinical recommendations can be made.The use of heat therapy should only be applied as part of a methodologically robust study to treat lymphoedema.

Transfusion of incompatible blood to a patient with alloanti-Sc1.

Sc1 is a high-prevalence blood group antigen that is part of the Scianna blood group system. The clinical significance of Scianna antibodies is not well understood because of their rarity; there are only a handful of cases in the literature. This scarcity of information can make it difficult to decide on the best course of action when transfusing a patient with alloantibodies to Scianna blood group antigens. We describe a case of an 85-year-old woman presenting with melena and a hemoglobin of 66 g/L. Upon request for crossmatched blood, a panreactive antibody was found, later elucidated to be alloanti-Sc1. Because of the urgent nature of the transfusion, the patient was transfused with 2 incompatible, presumed Sc1+, red blood cell units with no evidence of an acute or delayed transfusion reaction. This case has been shared with the International Society of Blood Transfusion Rare Donor Working Party, via their Outcome of Incompatible Transfusion form, and adds to the body of evidence on clinical significance of antibodies to the antigens of the Scianna blood group system.

Decoupling absorption and radiative cooling in mid-wave infrared bolometric elements.

We present a spectrally selective, passively cooled mid-wave infrared bolometric absorber engineered to spatially and spectrally decouple infrared absorption and thermal emission. The structure leverages an antenna-coupled metal-insulator-metal resonance for mid-wave infrared normal incidence photon absorption and a long-wave infrared optical phonon absorption feature, aligned closer to peak room temperature thermal emission. The phonon-mediated resonant absorption enables a strong long-wave infrared thermal emission feature limited to grazing angles, leaving the mid-wave infrared absorption feature undisturbed. The two independently controlled absorption/emission phenomena demonstrate decoupling of the photon detection mechanism from radiative cooling and offer a new design approach enabling ultra-thin, passively cooled mid-wave infrared bolometers.

H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment.

Silencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localized to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localization in an h1 mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase (Pol V). Loss of H1 resulted in heterochromatic TE enrichment by NRPE1. Increased NRPE1 binding was associated with increased chromatin accessibility in h1 , suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating an h1/nrpe1 double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions in h1 corresponded to loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposition correlated with increased methylation specifically in the CHH context. Additionally, we found that H1 restricts the occupancy of the methylation reader and activator complex component, SUVH1, indicating that H1's regulatory control of methylation pathways is not limited to RdDM. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.

DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis.

DNA methylation is a conserved epigenetic modification that is typically associated with silencing of transposable elements and promoter methylated genes. However, some DNA-methylated loci are protected from silencing, allowing transcriptional flexibility in response to environmental and developmental cues. Through a genetic screen in Arabidopsis (Arabidopsis thaliana), we uncovered an antagonistic relationship between the MICRORCHIDIA (MORC) protein and the IMITATION SWITCH (ISWI) complex in regulating the DNA-methylated SUPPRESSOR OF DRM1 DRM2 CMT3 (SDC) reporter. We demonstrate that components of the plant-specific ISWI complex, including CHROMATIN REMODELING PROTEIN11 (CHR11), CHR17, DDT-RELATED PROTEIN4 (DDR4), and DDR5, function to partially derepress silenced genes and transposable elements (TEs), through their function in regulating nucleosome distribution. This action also requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. Genome-wide studies revealed that DDR4 causes changes in nucleosome distribution at numerous loci, a subset of which is associated with changes in DNA methylation and/or transcription. Our work reveals a mechanism for balancing transcriptional flexibility and faithful silencing of DNA-methylated loci. As both ISWI and MORC family genes are widely distributed across plant and animal species, our findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic regulation.

MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions.

BACKGROUND: The microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC proteins act in the RNA-directed DNA methylation (RdDM) pathway, where they act as molecular tethers to ensure the efficient establishment of RdDM and de novo gene silencing. However, MORC proteins also have RdDM-independent functions although their underlying mechanisms are unknown. RESULTS: In this study, we examine MORC binding regions where RdDM does not occur in order to shed light on the RdDM-independent functions of MORC proteins. We find that MORC proteins compact chromatin and reduce DNA accessibility to transcription factors, thereby repressing gene expression. We also find that MORC-mediated repression of gene expression is particularly important under conditions of stress. MORC-regulated transcription factors can in some cases regulate their own transcription, resulting in feedback loops. CONCLUSIONS: Our findings provide insights into the molecular mechanisms of MORC-mediated chromatin compaction and transcription regulation.

Inclusion body myositis and dysphagia. Presentation, intervention and outcome at a swallowing clinic.

OBJECTIVE: This study reviewed patients with inclusion body myositis who were referred for assessment of dysphagia at a tertiary swallow clinic. It describes symptoms at presentation, imaging and management strategies. METHOD: A retrospective review of electronic patient records was performed between 2016 and 2020. RESULTS: Twenty-four patients were included, with a mean age of 72 years. Baseline modified Sydney Swallow Questionnaires identified problems with hard or dry food, food sticking, and repeated swallowing. Twenty-two patients had a Reflux Symptom Index score that could indicate significant reflux. Video swallow identified specific problems, including tongue base retraction (96 per cent) and residual pharyngeal pooling (92 per cent). Seven patients (30 per cent) had features of aspiration on imaging despite a median penetration-aspiration scale score of 2. Four patients received balloon dilatation, and two patients underwent cricopharyngeal myotomy. CONCLUSION: This study helped to profile features of dysphagia in patients with inclusion body myositis. More evidence is needed to determine the most effective management pathway for these patients.

Identification of potent and selective inhibitors of PKR via virtual screening and traditional design.

Protein Kinase RNA-activated (PKR) inhibition is thought to be relevant for immunology due to the potential to reduce macrophage and dendritic cell responses to bacteria and its signaling downstream of TNFα. PKR is also associated with neuroscience indications such as Alzheimer's disease due to its activation by the double stranded DNA (dsDNA) virus HSV1, a virus suggested to be important in the development of AD. Studies exploring the mechanistic role of PKR with existing tool molecules such as the tricyclic oxindole C16 are clouded by the poor selectivity profile of this ATP-competitive, Type I kinase inhibitor. Type II kinase leads such as the benzothiophene or pyrazolopyrimidine scaffolds from literature are equally poor in their selectivity profiles. As such, it became necessary to identify more potent and selective chemical matter to better understand PKR biology. A dual approach was taken. The first step of the strategy included virtual screening of the AbbVie compound collection. A combination of pharmacophore-based and GPU shape-based screening was pursued to identify selective chemical matter from promiscuous leads. The second step of the strategy followed traditional compound design. This step initiated from a literature lead with PKR cross reactivity. Combined, the two parallel efforts led to identification of more selective leads for investigation of PKR biology.

Terahertz Pulse Generation with Binary Phase Control in Nonlinear InAs Metasurface.

The effect of terahertz (THz) pulse generation has revolutionized broadband coherent spectroscopy and imaging at THz frequencies. However, THz pulses typically lack spatial structure, whereas structured beams are becoming essential for advanced spectroscopy applications. Nonlinear optical metasurfaces with nanoscale THz emitters can provide a solution by defining the beam structure at the generation stage. We develop a nonlinear InAs metasurface consisting of nanoscale optical resonators for simultaneous generation and structuring of THz beams. We find that THz pulse generation in the resonators is governed by optical rectification. It is more efficient than in ZnTe crystals, and it allows us to control the pulse polarity and amplitude, offering a platform for realizing binary-phase THz metasurfaces. To illustrate this capability, we demonstrate an InAs metalens, which simultaneously generates and focuses THz pulses. The control of spatiotemporal structure using nanoscale emitters opens doors for THz beam engineering and advanced spectroscopy and imaging applications.

Evaluation of mechanical cervical dislocation, captive bolt, carbon dioxide, and electrical methods for individual on-farm euthanasia of broiler breeders.

Efficacious euthanasia by applying manual cervical dislocation can be difficult on large and mature poultry. The challenge with using manual cervical dislocation is that the strength required to hold heavy poultry and swiftly apply cervical dislocation can be physically impossible for most people. Therefore, alternative methods of euthanasia are needed for mature and large poultry. Mechanical cervical dislocation using the Koechner Euthanizing Device (KED), captive bolt using the Turkey Euthanasia Device (TED), carbon dioxide (CO2), and electrical euthanasia were evaluated for use on 65-wk-old broiler breeders at flock termination. Following application of each method, physiological reflexes including the eye nictitating membrane reflex, mouth gaping, and body movement, broken skin, blood loss, kill success, time to cessation of heartbeat, and blood plasma corticosterone levels were assessed. Birds euthanized using the KED had longer response durations for eye nictitating membrane (91 s) and reflexive mouth gaping (161 s) compared to TED, CO2, and electrical euthanasia (0-7 s). Body movement durations were also longer for KED (214 s) and TED (209 s) than for CO2 and electrical euthanasia (0-8 s). The highest percentages of broken skin (93%) and blood loss (96%) were observed for TED, followed by KED (71%, 68%), then CO2 (0%, 6%) and electrical euthanasia (0%, 3%). No significant differences (P = 0.1781) were observed for kill success rates with 98% for KED, 100% for TED, 97% for CO2, and 100% for electrical euthanasia at 4-min. Time to heartbeat cessation did not differ between KED (659 s), TED (427 s), or CO2 (583 s) euthanasia methods. No heartbeat was detected following electrical euthanasia. Blood plasma corticosterone levels did not differ between preeuthanasia or posteuthanasia from any of the methods applied. Based on these results each euthanasia method is acceptable for use with broiler breeders.

Correction to "Terahertz Pulse Generation from GaAs Metasurfaces".

[This corrects the article DOI: 10.1021/acsphotonics.1c01908.].

Comparative analysis of the sensitivity of nanometallic thin film thermometers.

Thin film platinum resistive thermometers are conventionally applied for resistance thermometry techniques due to their stability and proven measurement accuracy. Depending upon the required thermometer thickness and temperature measurement, however, performance benefits can be realized through the application of alternative nanometallic thin films. Herein, a comparative experimental analysis is provided on the performance of nanometallic thin film thermometers most relevant to microelectronics and thermal sensing applications: Al, Au, Cu, and Pt. Sensitivity is assessed through the temperature coefficient of resistance, measured over a range of 10-300 K for thicknesses nominally spanning 25-200 nm. The interplay of electron scattering sources, which give rise to the temperature-dependent TCR properties for each metal, are analyzed in the framework of a Mayadas-Shatzkes based model. Despite the prevalence of evaporated Pt thin film thermometers, Au and Cu films fabricated in a similar manner may provide enhanced sensitivity depending upon thickness. These results may serve as a guide as the movement toward smaller measurement platforms necessitates the use of smaller, thinner metallic resistance thermometers.

Use of diamond sensors for a high-flux, high-rate X-ray pass-through diagnostic.

X-ray free-electron lasers (XFELs) deliver pulses of coherent X-rays on the femtosecond time scale, with potentially high repetition rates. While XFELs provide high peak intensities, both the intensity and the centroid of the beam fluctuate strongly on a pulse-to-pulse basis, motivating high-rate beam diagnostics that operate over a large dynamic range. The fast drift velocity, low X-ray absorption and high radiation tolerance properties of chemical vapour deposition diamonds make these crystals a promising candidate material for developing a fast (multi-GHz) pass-through diagnostic for the next generation of XFELs. A new approach to the design of a diamond sensor signal path is presented, along with associated characterization studies performed in the XPP endstation of the LINAC Coherent Light Source (LCLS) at SLAC. Qualitative charge collection profiles (collected charge versus time) are presented and compared with those from a commercially available detector. Quantitative results on the charge collection efficiency and signal collection times are presented over a range of approximately four orders of magnitude in the generated electron-hole plasma density.

Terahertz Pulse Generation from GaAs Metasurfaces.

Ultrafast optical excitation of select materials gives rise to the generation of broadband terahertz (THz) pulses. This effect has enabled the field of THz time-domain spectroscopy and led to the discovery of many physical mechanisms behind THz generation. However, only a few materials possess the required properties to generate THz radiation efficiently. Optical metasurfaces can relax stringent material requirements by shifting the focus onto the engineering of local electromagnetic fields to boost THz generation. Here we demonstrate the generation of THz pulses in a 160 nm thick nanostructured GaAs metasurface. Despite the drastically reduced volume, the metasurface emits THz radiation with efficiency comparable to that of a thick GaAs crystal. We reveal that along with classical second-order volume nonlinearity, an additional mechanism contributes strongly to THz generation in the metasurface, which we attribute to surface nonlinearity. Our results lay the foundation for engineering of semiconductor metasurfaces for efficient and versatile THz radiation emitters.

In Situ Ion Counting for Improved Implanted Ion Error Rate and Silicon Vacancy Yield Uncertainty.

An in situ counted ion implantation experiment improving the error on the number of ions required to form a single optically active silicon vacancy (SiV) defect in diamond 7-fold compared to timed implantation is presented. Traditional timed implantation relies on a beam current measurement followed by implantation with a preset pulse duration. It is dominated by Poisson statistics, resulting in large errors for low ion numbers. Instead, our in situ detection, measuring the ion number arriving at the substrate, results in a 2-fold improvement of the error on the ion number required to generate a single SiV compared to timed implantation. Through postimplantation analysis, the error is improved 7-fold compared to timed implantation. SiVs are detected by photoluminescence spectroscopy, and the yield of 2.98% is calculated through the photoluminescence count rate. Hanbury-Brown-Twiss interferometry is performed on locations potentially hosting single-photon emitters, confirming that 82% of the locations exhibit single photon emission statistics.

Clinical outcomes following pharyngolaryngectomy reconstruction: a 20-year single-centre study.

BACKGROUND: Advanced malignant neoplasms of the larynx and hypopharynx pose many therapeutic challenges. Total pharyngolaryngectomy and total laryngectomy provide an opportunity to cure these tumours but are associated with significant morbidity. Reconstruction of the pharyngeal defect following total pharyngolaryngectomy demands careful consideration and remains an area of debate within surgical discussions. METHODS: This paper describes a systemic analysis of pharyngeal reconstruction following total pharyngolaryngectomy and total laryngectomy, leveraging data collected over a 20-year period at a large tertiary referral centre. RESULTS: Analysing 155 patients, the results show that circumferential pharyngeal defects and prior radiotherapy have a significant impact on surgical complications. In addition, free tissue transfer in larger pharyngeal defects showed lower rates of post-operative anastomosis leak and stricture. CONCLUSION: Pharyngeal resection carries a substantial risk of post-operative complications, and free tissue transfer appears to be an effective means of reconstruction for circumferential defects.