Comparative landscape of genetic dependencies in human and chimpanzee stem cells.

Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell-cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells reshaped the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.

Comparative landscape of genetic dependencies in human and chimpanzee stem cells.

Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether changes in human cells alter requirements for essential genes. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells, providing support for the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells can reshape the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.

Patient-centered pharmacovigilance: priority actions from the inherited bleeding disorders community.

Pharmacovigilance, the science and practice of monitoring the effects of medicinals and their safety, is the responsibility of all stakeholders involved in the development, manufacture, regulation, distribution, prescription, and use of drugs and devices. The patient is the stakeholder most impacted by and the greatest source of information on safety issues. It is rare, however, for the patient to take a central role and exert leadership in the design and execution of pharmacovigilance. Patient organizations in the inherited bleeding disorders community are among the most established and empowered, particularly in the rare disorders. In this review, two of the largest bleeding disorders patient organizations, Hemophilia Federation of America (HFA) and National Hemophilia Foundation (NHF), offer insights into the priority actions required of all stakeholders to improve pharmacovigilance. The recent and ongoing increase in incidents raising safety concerns and a therapeutic landscape on the cusp of unprecedented expansion heighten the urgency of a recommitment to the primacy of patient safety and well-being in drug development and distribution. Plain Language Summary: Patients at the center of product safety Every medical device and therapeutic product has potential benefits and harms. The pharmaceutical and biomedical companies that develop them must demonstrate that they are effective, and the safety risks are limited or manageable, for regulators to approve them for use and sale. After the product has been approved and people are using it in their daily lives, it is important to continue to collect information about any negative side effects or adverse events; this is called pharmacovigilance. Regulators, like the United States (US) Food and Drug Administration, the companies that sell and distribute the products, and healthcare professionals who prescribe them are all required to participate in collecting, reporting, analyzing, and communicating this information. The people with the most firsthand knowledge of the benefits and harms of the drug or device are the patients who use them. They have an important responsibility to learn how to recognize adverse events, how to report them, and to stay informed of any news about the product from the other partners in the pharmacovigilance network. Those partners have a crucial responsibility to provide clear, easy-to-understand information to patients about any new safety concerns that come to light. The community of people with inherited bleeding disorders has recently encountered problems with poor communication of product safety issues, prompting two large US patient organizations, National Hemophilia Foundation and Hemophilia Federation of America, to hold a Safety Summit with all the pharmacovigilance network partners. Together they developed recommendations to improve the collection and communication of information about product safety so that patients can make well-informed, timely decisions about their use of drugs and devices. This article presents these recommendations in the context of how pharmacovigilance is supposed to work and some of the challenges encountered by the community.

Mapping cis- and trans-regulatory target genes of human-specific deletions.

Deletion of functional sequence is predicted to represent a fundamental mechanism of molecular evolution1,2. Comparative genetic studies of primates2,3 have identified thousands of human-specific deletions (hDels), and the cis-regulatory potential of short (≤31 base pairs) hDels has been assessed using reporter assays4. However, how structural variant-sized (≥50 base pairs) hDels influence molecular and cellular processes in their native genomic contexts remains unexplored. Here, we design genome-scale libraries of single-guide RNAs targeting 7.2 megabases of sequence in 6,358 hDels and present a systematic CRISPR interference (CRISPRi) screening approach to identify hDels that modify cellular proliferation in chimpanzee pluripotent stem cells. By intersecting hDels with chromatin state features and performing single-cell CRISPRi (Perturb-seq) to identify their cis- and trans-regulatory target genes, we discovered 19 hDels controlling gene expression. We highlight two hDels, hDel_2247 and hDel_585, with tissue-specific activity in the liver and brain, respectively. Our findings reveal a molecular and cellular role for sequences lost in the human lineage and establish a framework for functionally interrogating human-specific genetic variants.

Rethinking nomenclature for interspecies cell fusions.

Cell fusions have a long history of supporting biomedical research. These experimental models, historically referred to as 'somatic cell hybrids', involve combining the plasma membranes of two cells and merging their nuclei within a single cytoplasm. Cell fusion studies involving human and chimpanzee pluripotent stem cells, rather than somatic cells, highlight the need for responsible communication and a revised nomenclature. Applying the terms 'hybrid' and 'parental' to the fused and source cell lines, respectively, evokes reproductive relationships that do not exist between humans and other species. These misnomers become more salient in the context of fused pluripotent stem cells derived from different but closely related species. Here, we propose a precise, versatile and generalizable framework to describe these fused cell lines. We recommend the term 'composite cell line', to distinguish cell lines that are experimentally created through fusions from both reproductive hybrids and natural cell fusion events without obscuring the model in overly technical terms. For scientific audiences, we further recommend technical nomenclature that describes the contributing species, ploidy and cell type.

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.

Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.

A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA.

Bias dependent variability of low-frequency noise in single-layer graphene FETs.

Low-frequency noise (LFN) variability in graphene transistors (GFETs) is for the first time researched in this work under both experimental and theoretical aspects. LFN from an adequate statistical sample of long-channel solution-gated single-layer GFETs is measured in a wide range of operating conditions while a physics-based analytical model is derived that accounts for the bias dependence of LFN variance with remarkable performance. LFN deviations in GFETs stem from the variations of the parameters of the physical mechanisms that generate LFN, which are the number of traps (N tr) for the carrier number fluctuation effect (ΔN) due to trapping/detrapping process and the Hooge parameter (α H) for the mobility fluctuations effect (Δµ). ΔN accounts for an M-shape of normalized LFN variance versus gate bias with a minimum at the charge neutrality point (CNP) as it was the case for normalized LFN mean value while Δµ contributes only near the CNP for both variance and mean value. Trap statistical nature of the devices under test is experimentally shown to differ from classical Poisson distribution noticed at silicon-oxide devices, and this might be caused both by the electrolyte interface in GFETs under study and by the premature stage of the GFET technology development which could permit external factors to influence the performance. This not fully advanced GFET process growth might also cause pivotal inconsistencies affecting the scaling laws in GFETs of the same process.

Natural selection shaped the rise and fall of passenger pigeon genomic diversity.

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this disconnect, we analyzed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger pigeons' large population size appears to have allowed for faster adaptive evolution and removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These results demonstrate the effect that selection can have on a vertebrate genome and contradict results that suggested that population instability contributed to this species's surprisingly rapid extinction.

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.

BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA. RESULTS: We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage. CONCLUSIONS: AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.

Clear cell carcinoma, not otherwise specified/hyalinising clear cell carcinoma of the salivary gland: The current nomenclature, clinical/pathological characteristics and management.

Clear cell carcinoma, not otherwise specified (NOS)/hyalinising clear cell carcinoma (HCCC) is a rare entity in salivary gland tumour. The aim of the research is to review the current concepts and characteristics of this carcinoma. The clinical and pathological data of the disease obtained from literature and two original cases were analysed. Overall, 152 cases were reviewed up to the year 2014. The carcinomas were noted often in woman, in the seventh decade of life, located in oral cavity and as early-stages cancers. On pathological examination, they were characterized by tumour cells having clear cell morphology with hyalinised stroma. Immunohistochemical studies revealed that the carcinoma is positive for cytokeratin and negative for myoepithelial differentiation. EWSR1-ATF1 fusion is specific for the carcinoma. Also, 9% of the reported cases had local nodal metastasis, with 6 cases demonstrating distant metastases at presentation. On follow-up, 22% of patients had recurrent or with persistent diseases after surgery. The time for the first recurrence could be as long as 24 years. Risk factors for recurrence include advanced stage at diagnosis and metastases at presentation. To conclude, HCCC is a low grade malignancy but have the potential for local metastases, recurrence, distant metastases and cancer-related death.

Detecting hybridization using ancient DNA.

It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.

Neuromorphic Functions in PEDOT:PSS Organic Electrochemical Transistors.

Depressive short-term synaptic plasticity functions are implemented with a simple polymer poly(3,4ethylenedioxythiophene):poly(styrene sulfonate) ( PEDOT: PSS) organic electrochemical transistor device. These functions are a first step toward the realization of organic-based neuroinspired platforms with spatiotemporal information processing capabilities.

Punching Glass: A 10-Year Consecutive Series.

INTRODUCTION: Punching glass can cause severe and debilitating injuries. The literature is scant in regards to the injury patterns, optimal management, and preventative strategies. We have reviewed our experience of these injuries at a regional Australian hospital. METHODS: A retrospective chart review of all patients who had punched glass and presented to Cairns Base Hospital between January 2003 and December 2012. Data collected included age, gender, marital status, employment status, alcohol consumption, side of injury, intent, time of presentation, damaged structures, treatment required, operative time, total hospital stay, and required follow-up. RESULTS: 137 eligible patients were identified during the 10-year study period. Mean age was 26.3 years. Most were men (n = 113), single (n = 122), unemployed (n = 95), and intoxicated (n = 91). Most of these injuries presented outside of normal working hours (P < 0.001). Ninety-one patients had superficial skin lacerations only and did not require operative intervention. The remaining 46 patients had a total of 46 tendon, 18 muscle, 12 nerve, 8 vessel and 5 bone injuries, and all required operative intervention. Tendon, nerve and vessel injuries were strongly associated with each other (P < 0.05). CONCLUSIONS: This represents the largest case series of glass punching injuries in the English literature. Punching glass can cause significant morbidity in a young age group and is therefore a major public health concern. Thorough physical examination, appropriate imaging and operative repair can improve outcomes. Preventative measures such as stricter legislation and safety glass will reduce the burden of these injures on the individual and healthcare system in Australia.

An Unusual Cause of Dysphagia: A Large Expectorated Arteriovenous Malformation.

BACKGROUND: Vascular malformations are generally detected in childhood or adolescence with first presentations in adulthood being rare. CASE REPORT: We report the case of a 52-year-old female with threatened compromise of her airway after expectorating a massive arteriovenous malformation anchored at the supraglottis. The only preceding symptom was dysphagia. The lesion was resected, the patient had a quick recovery, and she has shown no evidence of recurrence. CONCLUSION: Although uncommon, vascular malformations of the supraglottis or hypopharynx should be considered in the differential diagnosis of a patient presenting with dysphagia because of the potential to cause disastrous airway compromise. Although a lesion presenting acutely mandates a definitive airway plan, when clinically possible, computed tomography scan and indirect laryngoscopy can provide useful information for the airway and operative teams.

Transtympanic Facial Nerve Paralysis: A Review of the Literature.

Facial nerve paralysis because of penetrating trauma through the external auditory canal is extremely rare, with a paucity of published literature. The objective of this study is to review the literature on transtympanic facial nerve paralysis and increase physician awareness of this uncommon injury through discussion of its clinical presentation, management and prognosis. We also aim to improve patient outcomes in those that have sustained this type of injury by suggesting an optimal management plan. In this case report, we present the case of a 46-year-old white woman who sustained a unilateral facial nerve paresis because of a garfish penetrating her tympanic membrane and causing direct damage to the tympanic portion of her facial nerve. On follow-up after 12 months, her facial nerve function has largely returned to normal. Transtympanic facial nerve paralysis is a rare injury but can have a favorable prognosis if managed effectively.

Concurrent Spigelian hernia and falciform ligament hernia in a 67-year-old female.

INTRODUCTION: Internal abdominal hernias account for 1% of all hernias but 5.8% of all bowel obstructions and hence are of significant clinical importance. Similarly Spigelian hernias account for only 0.12-2% of all abdominal wall hernias. CASE PRESENTATION: We present and discuss the management of a case that presented with concurrent falciform ligament internal abdominal hernia and Spigelian hernia. We believe this is the first reported case of such an occurrence in the literature. CONCLUSION: Due to the advancements in computer topography (CT) imaging many internal and Spigelian hernias are diagnosed pre-operatively though these scan are not always available or indicated in cases of suspected small bowel obstruction. Due to the high mortality rate of undiagnosed internal hernias a high clinical suspicion must be maintained. The authors recommend laparoscopic trans-abdominal repair of Spigelian hernias in order to examine the abdominal contents and exclude rare, though potentially serious internal hernias.

Electrical burn causing a unique pattern of neurological injury.

Neurological involvement is not uncommon in patients who sustain electrical injury. The exact mechanism of nervous system damage following electrical trauma is not fully understood. The gamut of possible neurologic manifestations following electrical injury is diverse. This case report describes a young man with a unique pattern of neurological injury following an electrical burn. The combination of brachial plexopathy, partial Horner's syndrome, and phrenic nerve palsy secondary to electrical injury has not been previously described in the literature.