The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development.

The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.

Phase separation and molecular ordering of the prion-like domain of the Arabidopsis thermosensory protein EARLY FLOWERING 3.

Liquid-liquid phase separation (LLPS) is an important mechanism enabling the dynamic compartmentalization of macromolecules, including complex polymers such as proteins and nucleic acids, and occurs as a function of the physicochemical environment. In the model plant, Arabidopsis thaliana, LLPS by the protein EARLY FLOWERING3 (ELF3) occurs in a temperature-sensitive manner and controls thermoresponsive growth. ELF3 contains a largely unstructured prion-like domain (PrLD) that acts as a driver of LLPS in vivo and in vitro. The PrLD contains a poly-glutamine (polyQ) tract, whose length varies across natural Arabidopsis accessions. Here, we use a combination of biochemical, biophysical, and structural techniques to investigate the dilute and condensed phases of the ELF3 PrLD with varying polyQ lengths. We demonstrate that the dilute phase of the ELF3 PrLD forms a monodisperse higher-order oligomer that does not depend on the presence of the polyQ sequence. This species undergoes LLPS in a pH- and temperature-sensitive manner and the polyQ region of the protein tunes the initial stages of phase separation. The liquid phase rapidly undergoes aging and forms a hydrogel as shown by fluorescence and atomic force microscopies. Furthermore, we demonstrate that the hydrogel assumes a semiordered structure as determined by small-angle X-ray scattering, electron microscopy, and X-ray diffraction. These experiments demonstrate a rich structural landscape for a PrLD protein and provide a framework to describe the structural and biophysical properties of biomolecular condensates.

The influence of social identity on attitudes toward wildlife.

Wildlife conservation depends on supportive social as well as biophysical conditions. Social identities such as hunter and nonhunter are often associated with different attitudes toward wildlife. However, it is unknown whether dynamics within and among these identity groups explain how attitudes form and why they differ. To investigate how social identities help shape wildlife-related attitudes and the implications for wildlife policy and conservation, we built a structural equation model with survey data from Montana (USA) residents (n = 1758) that tested how social identities affect the relationship between experiences with grizzly bears (Ursus arctos horribilis) and attitudes toward the species. Model results (r2  = 0.51) demonstrated that the hunter identity magnified the negative effect of vicarious property damage on attitudes toward grizzly bears (ß = -0.381, 95% confidence interval [CI]: -0.584 to -0.178, p < 0.001), which in turn strongly influenced acceptance (ß = -0.571, 95% CI: -0.611 to -0.531, p < 0.001). Our findings suggested that hunters' attitudes toward grizzly bears likely become more negative primarily because of in-group social interactions about negative experiences, and similar group dynamics may lead nonhunters to disregard the negative experiences that out-group members have with grizzly bears. Given the profound influence of social identity on human cognitions and behaviors in myriad contexts, the patterns we observed are likely important in a variety of wildlife conservation situations. To foster positive conservation outcomes and minimize polarization, management strategies should account for these identity-driven perceptions while prioritizing conflict prevention and promoting positive wildlife narratives within and among identity groups. This study illustrates the utility of social identity theory for explaining and influencing human-wildlife interactions.

La influencia de la identidad social sobre la actitud hacia la fauna Resumen La conservación de la fauna depende de condiciones de apoyo tanto sociales como biofísicas. La identidad social, como ser cazador o no, con frecuencia está asociada a las diferentes actitudes hacia la fauna. Sin embargo, no sabemos si las dinámicas dentro y entre estos grupos de identidad explican cómo las actitudes se forman y porqué son diferentes. Construimos un modelo de ecuación estructural con información de encuestas realizadas a 1,758 residentes de Montana (Estados Unidos) para conocer cómo la identidad social ayuda a formar la actitud relacionada con la fauna y las implicaciones que tiene para la conservación y políticas de fauna. El modelo analizó cómo la identidad social afecta la relación entre las experiencias con osos pardos (Ursus arctos horribilis) y la actitud hacia la especie. Los resultados del modelo (r2 = 0.51) demostraron que la identidad de cazador aumentaba el efecto negativo del daño indirecto a la propiedad sobre la actitud hacia los osos (ß=-0.381, 95% CI -0.584 a -0.178, p<0.001), lo cual en cambio tenía una gran influencia sobre la aceptación (ß=-0.571, 95% CI -0.611 a -0.531, p<0.001). Nuestros descubrimientos sugieren que la actitud de los cazadores hacia los osos probablemente se vuelve más negativa principalmente debido a las interacciones sociales del endogrupo en torno a las experiencias negativas; las dinámicas similares pueden llevar a los no cazadores a menospreciar las experiencias negativas que los miembros del exogrupo han tenido con los osos. Dada la influencia profunda que tiene la identidad social sobre la cognición humana y el comportamiento en una miríada de contextos, los patrones que observamos probablemente sean importantes en una variedad de situaciones de conservación de fauna. Para promover los resultados positivos de conservación y minimizar la polarización, las estrategias de manejo deberían considerar estas percepciones influenciadas por la identidad mientras se prioriza la prevención de conflictos y se promueven narrativas positivas de fauna dentro y entre los grupos de identidad. Este estudio demuestra la utilidad que tiene la teoría de identidad social para explicar e influenciar las interacciones humano-fauna.

Harm from Residential Indoor Air Contaminants.

This study presents a health-centered approach to quantify and compare the chronic harm caused by indoor air contaminants using disability-adjusted life-year (DALY). The aim is to understand the chronic harm caused by airborne contaminants in dwellings and identify the most harmful. Epidemiological and toxicological evidence of population morbidity and mortality is used to determine harm intensities, a metric of chronic harm per unit of contaminant concentration. Uncertainty is evaluated in the concentrations of 45 indoor air contaminants commonly found in dwellings. Chronic harm is estimated from the harm intensities and the concentrations. The most harmful contaminants in dwellings are PM2.5, PM10-2.5, NO2, formaldehyde, radon, and O3, accounting for over 99% of total median harm of 2200 DALYs/105 person/year. The chronic harm caused by all airborne contaminants in dwellings accounts for 7% of the total global burden from all diseases.

Quantitative analysis of intestinal perfusion with indocyanine green (ICG) and methylene blue (MB) using a single clinically approved fluorescence imaging system: a demonstration in a porcine model.

BACKGROUND: Near-infrared fluorescence (NIRF) angiography with intraoperative administration of indocyanine green (ICG) has rapidly disseminated in clinical practice. Another clinically approved, and widely available dye, methylene blue (MB), has up to now not been used for this purpose. Recently, we demonstrated promising results for the real-time evaluation of intestinal perfusion using this dye. The primary aim of this study was to perform a quantitative analysis of bowel perfusion assessment for both ICG and MB. METHODS: Four mature female Landrace pigs underwent laparotomy under general anesthesia. An ischemic bowel loop with five regions of interest (ROIs) with varying levels of perfusion was created in each animal. An intravenous (IV) injection of 0.25 mg/kg-0.50 mg/kg MB was administered after 10 min, followed by NIRF imaging in MB mode and measurement of local lactate levels in all corresponding ROIs. This procedure was repeated in ICG mode (IV dose of 0.2 mg/kg) after 60 min. The quest spectrum fluorescence camera (Quest Medical Imaging, Middenmeer, The Netherlands) was used for NIRF imaging of both MB and ICG. RESULTS: Intraoperative NIRF imaging of bowel perfusion assessment with MB and ICG was successful in all studied animals. Ingress (i/s) levels were calculated and correlated with local lactate levels. Both MB and ICG ingress values showed a significant negative correlation (r = - 0.7709; p = < 0.001; r = - 0.5367, p = 0.015, respectively) with local lactate levels. This correlation was stronger for MB compared to ICG, although ICG analysis showed higher absolute ingress values. CONCLUSION: Our fluorescence quantification analysis validates the potential to use MB for bowel perfusion assessment besides the well-known and widely used ICG. Further human studies are necessary to translate our findings to clinical applications.

Towards an Analytical Biology.

This article draws a perspective on the increasingly unavoidable question of whether steps can be taken in genomics and biology at large to move them more rapidly towards more analytical and deductive biology, akin to similar developments that occurred in other natural sciences, such as physics and chemistry, centuries ago. It provides a summary of recent advances in other relevant sciences in the last 3 decades that are likely to pull it in that direction in the next decade or so, as well as what methods and tools will make it possible.

A multicentre double-blinded randomized controlled trial on the efficacy of laser-assisted hatching in patients with repeated implantation failure undergoing IVF or ICSI.

STUDY QUESTION: Does assisted hatching increase the cumulative live birth rate in subfertile couples with repeated implantation failure? SUMMARY ANSWER: This study showed no evidence of effect for assisted hatching as an add-on in subfertile couples with repeated implantation failure. WHAT IS KNOWN ALREADY: The efficacy of assisted hatching, with regard to the live birth rate has not been convincingly demonstrated in randomized trials nor meta-analyses. It is suggested though that especially poor prognosis women, e.g. women with repeated implantation failure, might benefit most from assisted hatching. STUDY DESIGN, SIZE, DURATION: The study was designed as a double-blinded, multicentre randomized controlled superiority trial. In order to demonstrate a statistically significant absolute increase in live birth rate of 10% after assisted hatching, 294 participants needed to be included per treatment arm, being a total of 588 subfertile couples. Participants were included and randomized from November 2012 until November 2017, 297 were allocated to the assisted hatching arm of the study and 295 to the control arm. Block randomization in blocks of 20 participants was applied and randomization was concealed from participants, treating physicians, and laboratory staff involved in the embryo transfer procedure. Ovarian hyperstimulation, oocyte retrieval, laboratory procedures, embryo selection for transfer and cryopreservation, the transfer itself, and luteal support were performed according to local protocols and were identical in both the intervention and control arm of the study with the exception of the assisted hatching procedure which was only performed in the intervention group. The laboratory staff performing the assisted hatching procedure was not involved in the embryo transfer itself. PARTICIPANTS/MATERIALS, SETTING, METHODS: Participants were eligible for inclusion in the study after having had either at least two consecutive fresh IVF or ICSI embryo transfers, including the transfer of frozen and thawed embryos originating from those fresh cycles, and which did not result in a pregnancy or as having had at least one fresh IVF or ICSI transfer and at least two frozen embryo transfers with embryos originating from that fresh cycle which did not result in a pregnancy. The study was performed at the laboratory sites of three tertiary referral hospitals and two university medical centres in the Netherlands. MAIN RESULTS AND THE ROLE OF CHANCE: The cumulative live birth rate per started cycle, including the transfer of fresh and subsequent frozen/thawed embryos if applicable, resulted in 77 live births in the assisted hatching group (n = 297, 25.9%) and 68 live births in the control group (n = 295, 23.1%). This proved to be statistically not significantly different (relative risk: 1.125, 95% CI: 0.847 to 1.494, P = 0.416). LIMITATIONS, REASONS FOR CAUTION: There was a small cohort of subfertile couples that after not achieving an ongoing pregnancy, still had cryopreserved embryos in storage at the endpoint of the trial, i.e. 1 year after the last randomization. It cannot be excluded that the future transfer of these frozen/thawed embryos increases the cumulative live birth rate in either or both study arms. Next, at the start of this study, there was no international consensus on the definition of repeated implantation failure. Therefore, it cannot be excluded that assisted hatching might be effective in higher order repeated implantation failures. WIDER IMPLICATIONS OF THE FINDINGS: This study demonstrated no evidence of a statistically significant effect for assisted hatching by increasing live birth rates in subfertile couples with repeated implantation failure, i.e. the couples which, based on meta-analyses, are suggested to benefit most from assisted hatching. It is therefore suggested that assisted hatching should only be offered if information on the absence of evidence of effect is provided, at no extra costs and preferably only in the setting of a clinical trial taking cost-effectiveness into account. STUDY FUNDING/COMPETING INTEREST(S): None. TRIAL REGISTRATION NUMBER: Netherlands Trial Register (NTR 3387, NL 3235, https://www.clinicaltrialregister.nl/nl/trial/26138). TRIAL REGISTRATION DATE: 6 April 2012. DATE OF FIRST PATIENT'S ENROLMENT: 28 November 2012.

The accuracy of cystoscopy in predicting muscle invasion in newly diagnosed bladder cancer patients.

PURPOSE: The prognosis of muscle-invasive bladder cancer (MIBC) has not improved for three decades. Transurethral resection of the bladder tumor (TURBT) is the standard procedure for local tumor staging. TURBT has several limitations, including the spread of tumor cells. Therefore, an alternative is needed in patients with suspected MIBC. Recent studies have shown that mpMRI is very accurate in staging bladder tumors. Because the diagnostic efficacy of urethrocystoscopy (UCS) has been reported as good as the efficacy of mpMRI to predict muscle invasion we performed this prospective multicenter study in which we compare UCS with pathology. METHODS: From July 2020 until March 2022, 321 patients with suspected primary BC in seven participating Dutch hospitals were included in this study. A flexible UCS was performed by urologists, physician assistants, or residents. Predictions of muscle invasion using a 5-point Likert scale alongside the histopathology data were recorded. The sensitivity, specificity, predictive values, and 95% confidence intervals were determined using a standard contingency table. RESULTS: Of the 321 included patients, 232 (72.3%) received a histopathological diagnosis of non-muscle-invasive bladder cancer (NMIBC) and 71 (22.1%) were histopathologically diagnosed as MIBC. In 2 patients (0.6%), classification was not possible (Tx). Cystoscopy predicted muscle invasion with a sensitivity of 71.8% (95% CI 59.9-81.9), and a specificity of 89.9% (95% CI 85.4-93.3). This corresponds to a positive predictive value (PPV) of 67.1% and a negative predictive value (NPV) of 91.7%. CONCLUSION: Our study shows a moderate accuracy of cystoscopy to predict muscle invasion. This result does not support the use of cystoscopy only instead of TURBT for local staging.

International survey among surgeons on the perioperative management of rectal cancer.

BACKGROUND: Several pivotal studies and international guidelines on the perioperative management of rectal cancer have been published. However, little is known about the current state of perioperative management of rectal cancer patients in clinical practice worldwide. METHODS: An online survey including 13 questions focusing on key topics related to the perioperative management of patients with rectal cancer was conducted among colorectal surgeons registered within the database of the Research Institute Against Digestive Cancer (IRCAD). RESULTS: A total of 535 respondents from 89 countries participated in the survey. Most surgeons worked in the European region (40.9%). Two hundred and fifty-four respondents (47.5%) performed less than 25% of surgical procedures laparoscopically. The most commonly used definition of the upper limit of the rectum was a fixed distance from the anal verge (23.4%). Magnetic resonance imaging was used to define the upper limit of the rectum by 258 respondents (48.2%). During total mesorectal excision (TME), 301 respondents (56.3%) used a high-tie technique. The most commonly constructed anastomosis was an end-to-end anastomosis (68.2%) with the majority of surgeons performing a leak test intraoperatively (88.9%). A total of 355 respondents (66.4%) constructed a diverting ostomy, and the majority of these surgeons constructed an enterostomy (82%). A total of 208 respondents (39.3%) closed a stoma within 8 weeks. Lastly, 135 respondents (25.2%) introduced a solid diet on postoperative day 1. CONCLUSION: There is considerable heterogeneity in the perioperative management of rectal cancer patients worldwide with several discrepancies between current international practice and recommendations from international guidelines. To achieve worldwide standardization in rectal cancer care, further research is needed to elucidate the cause of this heterogeneity and find ways of improved implementation of best practice recommendations.

Simultaneous fluorescence imaging of bowel perfusion and ureter delineation using methylene blue: a demonstration in a porcine model.

BACKGROUND: Intraoperative near-infrared fluorescence imaging (NIRF) with preoperative optical dye administration is a promising technique for quick and easy intraoperative visualization of the ureter and for an improved, real-time assessment of intestinal perfusion. During colorectal surgery, there is a need for simultaneous non-invasive ureteral imaging and bowel perfusion assessment, using one single camera system. The purpose of this study is to investigate the feasibility of simultaneous intestinal perfusion and ureteral imaging using a single commercially available NIRF imaging system. METHODS: Six Landrace pigs underwent laparotomy under general anesthesia in this experiment. An intravenous (IV) dose of 0.2 mg/kg indocyanine green (ICG) was given to assess bowel perfusion. Two pairs received a methylene blue (MB) iv injection of 0.75, 0.50 or 0.25 mg/kg respectively to investigate ureteral visualization. Quest Spectrum Fluorescence Camera (Quest Medical Imaging, Middenmeer, The Netherlands) was used for NIRF imaging. RESULTS: Ureter visualization and bowel perfusion under NIRF imaging was achieved in all animals. All ureters were visible after five to ten minutes and remained clearly visible until the end of every experiment (120-420 min). A mixed model analysis did not show any significant differences neither between the three groups nor over time. Importantly, we demonstrated that bowel perfusion could be visualized with methylene blue (MB) as well. We observed no interference between ICG and MB and a faster washout of MB. CONCLUSION: We successfully demonstrated simultaneous fluorescence angiography with ICG and ureteral imaging with MB in the same surgical procedure, with the same commercially available NIRF imaging equipment. More importantly, we showed that the use MB is adequate for bowel perfusion assessment and ureter visualization with this NIRF imaging system. Besides, MB showed an earlier washout time, which can be clinical beneficial as a repeated dye injection may be necessary during a surgical procedure.

Signing at the beginning versus at the end does not decrease dishonesty.

Honest reporting is essential for society to function well. However, people frequently lie when asked to provide information, such as misrepresenting their income to save money on taxes. A landmark finding published in PNAS [L. L. Shu, N. Mazar, F. Gino, D. Ariely, M. H. Bazerman, Proc. Natl. Acad. Sci. U.S.A. 109, 15197-15200 (2012)] provided evidence for a simple way of encouraging honest reporting: asking people to sign a veracity statement at the beginning instead of at the end of a self-report form. Since this finding was published, various government agencies have adopted this practice. However, in this project, we failed to replicate this result. Across five conceptual replications (n = 4,559) and one highly powered, preregistered, direct replication (n = 1,235) conducted with the authors of the original paper, we observed no effect of signing first on honest reporting. Given the policy applications of this result, it is important to update the scientific record regarding the veracity of these results.

Molecular mechanisms of Evening Complex activity in Arabidopsis.

The Evening Complex (EC), composed of the DNA binding protein LUX ARRHYTHMO (LUX) and two additional proteins EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light entrainment, acting as an important environmental sensor and conveying this information to growth and developmental pathways. However, the molecular basis for EC DNA binding specificity and temperature-dependent activity were not known. Here, we solved the structure of the DNA binding domain of LUX in complex with DNA. Residues critical for high-affinity binding and direct base readout were determined and tested via site-directed mutagenesis in vitro and in vivo. Using extensive in vitro DNA binding assays of LUX alone and in complex with ELF3 and ELF4, we demonstrate that, while LUX alone binds DNA with high affinity, the LUX-ELF3 complex is a relatively poor binder of DNA. ELF4 restores binding to the complex. In vitro, the full EC is able to act as a direct thermosensor, with stronger DNA binding at 4 °C and weaker binding at 27 °C. In addition, an excess of ELF4 is able to restore EC binding even at 27 °C. Taken together, these data suggest that ELF4 is a key modulator of thermosensitive EC activity.

A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies.

Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause neurodevelopmental disorders (NDDs). Here, we report on five individuals with mutations in SMARCD1; the individuals present with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet. Trio exome sequencing proved the mutations to be de novo in four of the five individuals. Mutations in other SWI/SNF components cause Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, or other syndromic and non-syndromic NDDs. Although the individuals presented here have dysmorphisms and some clinical overlap with these syndromes, they lack their typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog Bap60 in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom-body-specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify an NDD caused by SMARCD1 mutations and establish a role for the SMARCD1 ortholog Bap60 in the regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development when neuronal circuits that are required for learning and memory are formed.

Distinguishing post-translational modifications in dominantly inherited frontotemporal dementias: FTLD-TDP Type A (GRN) vs Type B (C9orf72).

AIMS: Frontotemporal dementias are neuropathologically characterised by frontotemporal lobar degeneration (FTLD). Intraneuronal inclusions of transactive response DNA-binding protein 43 kDa (TDP-43) are the defining pathological hallmark of approximately half of the FTLD cases, being referred to as FTLD-TDP. The classification of FTLD-TDP into five subtypes (Type A to Type E) is based on pathologic phenotypes; however, the molecular determinants underpinning the phenotypic heterogeneity of FTLD-TDP are not well known. It is currently undetermined whether TDP-43 post-translational modifications (PTMs) may be related to the phenotypic diversity of the FTLDs. Thus, the investigation of FTLD-TDP Type A and Type B, associated with GRN and C9orf72 mutations, becomes essential. METHODS: Immunohistochemistry was used to identify and map the intraneuronal inclusions. Sarkosyl-insoluble TDP-43 was extracted from brains of GRN and C9orf72 mutation carriers post-mortem and studied by Western blot analysis, immuno-electron microscopy and mass spectrometry. RESULTS: Filaments of TDP-43 were present in all FTLD-TDP preparations. PTM profiling identified multiple phosphorylated, N-terminal acetylated or otherwise modified residues, several of which have been identified for the first time as related to sarkosyl-insoluble TDP-43. Several PTMs were specific for either Type A or Type B, while others were identified in both types. CONCLUSIONS: The current results provide evidence that the intraneuronal inclusions in the two genetic diseases contain TDP-43 filaments. The discovery of novel, potentially type-specific TDP-43 PTMs emphasises the need to determine the mechanisms leading to filament formation and PTMs, and the necessity of exploring the validity and occupancy of PTMs in a prognostic/diagnostic setting.

Loss of ANCO1 repression at AIB1/YAP targets drives breast cancer progression.

Transcription factors critical for the transition of normal breast epithelium to ductal carcinoma in situ (DCIS) and invasive breast cancer are not clearly defined. Here, we report that the expression of a subset of YAP-activated and YAP-repressed genes in normal mammary and early-stage breast cancer cells is dependent on the nuclear co-activator AIB1. Gene expression, sequential ChIP, and ChIP-seq analyses show that AIB1 and YAP converge upon TEAD for transcriptional activation and repression. We find that AIB1-YAP repression of genes at the 1q21.3 locus is mediated by AIB1-dependent recruitment of ANCO1, a tumor suppressor whose expression is progressively lost during breast cancer progression. Reducing ANCO1 reverts AIB1-YAP-dependent repression, increases cell size, and enhances YAP-driven aberrant 3D growth. Loss of endogenous ANCO1 occurs during DCIS xenograft progression, a pattern associated with poor prognosis in human breast cancer. We conclude that increased expression of AIB1-YAP co-activated targets coupled with a loss of normal ANCO1 repression is critical to patterns of gene expression that mediate malignant progression of early-stage breast cancer.

Index Coding with Multiple Interpretations.

The index coding problem consists of a system with a server and multiple receivers with different side information and demand sets, connected by a noiseless broadcast channel. The server knows the side information available to the receivers. The objective is to design an encoding scheme that enables all receivers to decode their demanded messages with a minimum number of transmissions, referred to as an index code length. The problem of finding the minimum length index code that enables all receivers to correct a specific number of errors has also been studied. This work establishes a connection between index coding and error-correcting codes with multiple interpretations from the tree construction of nested cyclic codes. The notion of multiple interpretations using nested codes is as follows: different data packets are independently encoded, and then combined by addition and transmitted as a single codeword, minimizing the number of channel uses and offering error protection. The resulting packet can be decoded and interpreted in different ways, increasing the error correction capability, depending on the amount of side information available at each receiver. Motivating applications are network downlink transmissions, information retrieval from datacenters, cache management, and sensor networks.

Classifying single nucleotide polymorphisms in humans.

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation amongst the human population and are key to personalized medicine. New tests are presented to distinguish pathogenic/malign (i.e., likely to contribute to or cause a disease) from nonpathogenic/benign SNPs, regardless of whether they occur in coding (exon) or noncoding (intron) regions in the human genome. The tests are based on the nearest neighbor (NN) model of Gibbs free energy landscapes of DNA hybridization and on deep structural properties of DNA revealed by an approximating metric (the h-distance) in DNA spaces of oligonucleotides of a common size. The quality assessments show that the newly defined PNPG test can classify a SNP with an accuracy about 73% for the required parameters. The best performance among machine learning models is a feed-forward neural network with fivefold cross-validation accuracy of at least 73%. These results may provide valuable tools to solve the SNP classification problem, where tools are lacking, to assess the likelihood of disease causing in unclassified SNPs. These tests highlight the significance of hybridization chemistry in SNPs. They can be applied to further the effectiveness of research in the areas of genomics and metabolomics.

Free-breathing abdominal T1 mapping using an optimized MR fingerprinting sequence.

In this work, we propose a free-breathing magnetic resonance fingerprinting (MRF) method that can be used to obtain B1+ -robust quantitative T1 maps of the abdomen in a clinically acceptable time. A three-dimensional MRF sequence with a radial stack-of-stars trajectory was implemented, and its k-space acquisition ordering was adjusted to improve motion-robustness in the context of MRF. The flip angle pattern was optimized using the Cramér-Rao Lower Bound, and the encoding efficiency of sequences with 300, 600, 900 and 1800 flip angles was evaluated. To validate the sequence, a movable multicompartment phantom was developed. Reference multiparametric maps were acquired under stationary conditions using a previously validated MRF method. Periodic motion of the phantom was used to investigate the motion-robustness of the proposed sequence. The best performing sequence length (600 flip angles) was used to image the abdomen during a free-breathing volunteer scan. When using a series of 600 or more flip angles, the estimated T1 values in the stationary phantom showed good agreement with the reference scan. Phantom experiments revealed that motion-related artifacts can appear in the quantitative maps and confirmed that a motion-robust k-space ordering is essential. The in vivo scan demonstrated that the proposed sequence can produce clean parameter maps while the subject breathes freely. Using this sequence, it is possible to generate B1+ -robust quantitative maps of T1 and B1+ next to M0 -weighted images under free-breathing conditions at a clinically usable resolution within 5 min.

Meridionella gen. nov., a New Genus of Cystocloniaceae (Gigartinales, Rhodophyta) from the Southern Hemisphere, Including M. obtusangula comb. nov. and M. antarctica sp. nov.

The classification of Cystoclonium obtusangulum has been questioned since the species was first described by Hooker and Harvey as Gracilaria? obtusangula. The objective of this study was to provide the first comprehensive taxonomic analysis of Cystoclonium obtusangulum, based on DNA sequences coupled with morphological observations made on syntype specimens and new collections. Sequence divergences of rbcL, UPA, and COI-5P, and maximum-likelihood phylogenies for rbcL and 18S demonstrated that specimens identified as Cystoclonium obtusangulum represent a clade of two distinct species that are distantly related to the generitype Cystoclonium purpureum. A new genus, Meridionella gen. nov., is proposed for this clade. The two species placed in this new genus were morphologically indistinguishable cryptic species, but have disjunct distributions, with Meridionella obtusangula comb. nov. found from temperate to cold coasts of South America and the Falkland Islands and Meridionella antarctica sp. nov., occurring in Antarctic waters. Vegetative and reproductive characters of Meridionella gen. nov. are described, and implications of our results for the biogeography of the family Cystocloniaceae are discussed.

Prosthodontic rehabilitation of head and neck cancer patients-Challenges and new developments.

Head and neck cancer treatment can severely alter oral function and aesthetics, and reduce quality of life. The role of maxillofacial prosthodontists in multidisciplinary treatment of head and neck cancer patients is essential when it comes to oral rehabilitation and its planning. This role should preferably start on the day of first intake. Maxillofacial prosthodontists should be involved in the care pathway to shape and outline the prosthetic and dental rehabilitation in line with the reconstructive surgical options. With the progress of three-dimensional technology, the pretreatment insight in overall prognosis and possibilities of surgical and/or prosthetic rehabilitation has tremendously increased. This increased insight has helped to improve quality of cancer care. This expert review addresses the involvement of maxillofacial prosthodontists in treatment planning, highlighting prosthodontic rehabilitation of head and neck cancer patients from start to finish.