TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing.

BACKGROUND: High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, 'N's. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address 'N's correctly or efficiently. RESULTS: Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base 'N's, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage. CONCLUSIONS: The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.

Uncovering the neural control of laryngeal activity and subglottic pressure in anaesthetized rats: insights from mesencephalic regions.

To assess the possible interactions between the dorsolateral periaqueductal gray matter (dlPAG) and the different domains of the nucleus ambiguus (nA), we have examined the pattern of double-staining c-Fos/FoxP2 protein immunoreactivity (c-Fos-ir/FoxP2-ir) and tyrosine hydroxylase (TH) throughout the rostrocaudal extent of nA in spontaneously breathing anaesthetised male Sprague-Dawley rats during dlPAG electrical stimulation. Activation of the dlPAG elicited a selective increase in c-Fos-ir with an ipsilateral predominance in the somatas of the loose (p < 0.05) and compact formation (p < 0.01) within the nA and confirmed the expression of FoxP2 bilaterally in all the domains within the nA. A second group of experiments was made to examine the importance of the dlPAG in modulating the laryngeal response evoked after electrical or chemical (glutamate) dlPAG stimulations. Both electrical and chemical stimulations evoked a significant decrease in laryngeal resistance (subglottal pressure) (p < 0.001) accompanied with an increase in respiratory rate together with a pressor and tachycardic response. The results of our study contribute to new data on the role of the mesencephalic neuronal circuits in the control mechanisms of subglottic pressure and laryngeal activity.

Fifth Edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues: Acute Lymphoblastic Leukemias, Mixed-Phenotype Acute Leukemias, Myeloid/Lymphoid Neoplasms With Eosinophilia, Dendritic/Histiocytic Neoplasms, and Genetic Tumor Syndromes.

This manuscript represents a review of lymphoblastic leukemia/lymphoma (acute lymphoblastic leukemia/lymphoblastic lymphoma), acute leukemias of ambiguous lineage, mixed-phenotype acute leukemias, myeloid/lymphoid neoplasms with eosinophilia and defining gene rearrangements, histiocytic and dendritic neoplasms, and genetic tumor syndromes of the 5th edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues. The diagnostic, clinicopathologic, cytogenetic, and molecular genetic features are discussed. The differences in comparison to the 4th revised edition of the World Health Organization classification of hematolymphoid neoplasms are highlighted.

A novel method to assess copy number variations in melanocytic neoplasms: Droplet digital PCR for precise quantitation of MYC and MYB genes.

INTRODUCTION: While most melanocytic neoplasms can be classified as either benign or malignant by histopathology alone, ancillary molecular diagnostic tests can be necessary to establish the correct diagnosis in challenging cases. Currently, the detection of copy number variations (CNVs) by fluorescence in situ hybridization and chromosomal microarray (CMA) are the most popular methods, but remain expensive and inaccessible. We aim to develop a relatively inexpensive, fast, and accessible molecular assay to detect CNVs relevant to melanoma using droplet digital polymerase chain reaction (ddPCR) technology. METHODS: In this proof-of-concept study, we evaluated CNVs in MYC and MYB genes from 73 cases of benign nevi, borderline melanocytic lesions, and primary and metastatic melanoma at our institution from 2015 to 2022. A multiplexed ddPCR assay and CMA were performed on each sample, and the results were compared. RESULTS: Concordance analysis of ddPCR with CMA for quantification of MYC and MYB CNVs revealed a sensitivity and specificity of 89% and 86% for MYC and 83% and 74% for MYB, respectively. CONCLUSION: We demonstrate the first use of a multiplexed ddPCR assay to identify CNVs in melanocytic neoplasms. With further improvement and validation, ddPCR may represent a low-cost and rapid tool to aid in the diagnosis of histopathologically ambiguous melanocytic tumors.

Abnormal ambiguous facial expression recognition in Chinese patients with schizophrenia.

BACKGROUND: Patients with schizophrenia (SCZ) exhibit difficulties deficits in recognizing facial expressions with unambiguous valence. However, only a limited number of studies have examined how these patients fare in interpreting facial expressions with ambiguous valence (for example, surprise). Thus, we aimed to explore the influence of emotional background information on the recognition of ambiguous facial expressions in SCZ. METHODS: A 3 (emotion: negative, neutral, and positive) × 2 (group: healthy controls and SCZ) experimental design was adopted in the present study. The experimental materials consisted of 36 images of negative emotions, 36 images of neutral emotions, 36 images of positive emotions, and 36 images of surprised facial expressions. In each trial, a briefly presented surprised face was preceded by an affective image. Participants (36 SCZ and 36 healthy controls (HC)) were required to rate their emotional experience induced by the surprised facial expressions. Participants' emotional experience was measured using the 9-point rating scale. The experimental data have been analyzed by conducting analyses of variances (ANOVAs) and correlation analysis. RESULTS: First, the SCZ group reported a more positive emotional experience under the positive cued condition compared to the negative cued condition. Meanwhile, the HC group reported the strongest positive emotional experience in the positive cued condition, a moderate experience in the neutral cued condition, and the weakest in the negative cue condition. Second, the SCZ (vs. HC) group showed longer reaction times (RTs) for recognizing surprised facial expressions. The severity of schizophrenia symptoms in the SCZ group was negatively correlated with their rating scores for emotional experience under neutral and positive cued condition. CONCLUSIONS: Recognition of surprised facial expressions was influenced by background information in both SCZ and HC, and the negative symptoms in SCZ. The present study indicates that the role of background information should be fully considered when examining the ability of SCZ to recognize ambiguous facial expressions.

Facial impressions of niceness influence children's interpretations of peers' ambiguous behavior.

Children infer personality traits from faces when they are asked explicitly which face appears nice or mean. Less is known about how children use face-trait information implicitly to make behavioral evaluations. We used the Ambiguous Situations Protocol to explore how children use face-trait information to form interpretations of ambiguous situations when the behavior or intention of the target child was unclear. On each trial, children (N = 144, age range = 4-11.95 years; 74 girls, 67 boys, 3 gender not specified; 70% White, 10% other or mixed race, 5% Asian, 4% Black, 1% Indigenous, 9% not specified) viewed a child's face (previously rated high or low in niceness) before seeing the child's face embedded within an ambiguous scene (Scene Task) or hearing a vignette about a misbehavior done by that child (Misbehavior Task). Children described what was happening in each scene and indicated whether each misbehavior was done on purpose or by accident. Children also rated the behavior of each child and indicated whether the child would be a good friend. Facial niceness influenced children's interpretations of ambiguous behavior (Scene Task) by 4 years of age, and ambiguous intentions (Misbehavior Task) by 6 years. Our results suggest that the use of face-trait cues to form interpretations of ambiguous behavior emerges early in childhood, a bias that may lead to differential treatment for peers perceived with a high-nice face versus a low-nice face.

A novel troubleshooting technique for below-the-knee artery occlusions with proximal cap ambiguity: Transpedal Retrograde Wire Just Marker Technique.

BACKGROUND: Chronic total occlusions with ambiguous proximal caps pose a challenging problem in below-the-knee artery endovascular interventions. CASE REPORT: We defined a new technique for antegrade puncture and penetration of an ambiguous proximal cap in a 52-year old male patient with a non-healing wound on his right forefoot. Anterior tibial artery (ATA) was determined as the target vessel; however, its origin and course could not be determined. A retrograde guidewire (Asahi Gladius 0.018 inch, Asahi Intecc) was advanced into the distal ATA via transpedal loop following pedal loop angioplasty. This guidewire was advanced through and parked to the tibioperoneal trunk with a small distal loop at the tip. While the looped wire was held in its position as a marker for ATA ostium, a second guidewire (Asahi Gladius 0.018 inch, Asahi Intecc) with the guidance of 4F vertebral catheter (Vert Catheter, Merit Medical) successfully penetrated the ambiguous cap and subsequent target vessel revascularization was achieved with 2.5/150 mm peripheral balloon angioplasty catheter (Minerva SC 0.018 inch, BrosMed Medical). CONCLUSION: Transpedal Retrograde Wire Just Marker Technique is a novel and practical technique which can be used in chronic total occlusions of below-the-knee arteries with ambiguous proximal caps.

LGBTQ+ disclosure: challenges and possibilities.

This paper uses Ambiguous Loss Theory to explore the anticipatory and ambiguous losses and stressors surrounding the decision to come out as Lesbian, Gay, Bisexual, Transgender or Queer. Purposive sampling was used to administer a survey to 429 individuals who identified as LGBTQ+ about their coming out decisions and experiences. Data were coded and three major themes were developed: (1) the need for psychosocial safety (fear of being disowned, shunned or abandoned); (2) experiences of anxiety, depression, emotional stress, and shame; and (3) the pursuit of authenticity, self-discovery and liberation. Findings from the study indicate that coming out for LGBTQ+ individuals in the twenty first century remains accompanied by challenges and fears, both before and after the process, which significantly affects individuals' health and safety. In the longer term, despite the challenges, stressors and losses identified by participants, most reported that disclosing their sexual orientation had greatly improved their health and mental well-being.

Effects of two different social exclusion paradigms on ambiguous facial emotion recognition.

Social exclusion is an emotionally painful experience that leads to various alterations in socio-emotional processing. The perceptual and emotional consequences that may arise from experiencing social exclusion can vary depending on the paradigm used to manipulate it. Exclusion paradigms can vary in terms of the severity and duration of the leading exclusion experience, thereby classifying it as either a short-term or long-term experience. The present study aimed to study the impact of exclusion on socio-emotional processing using different paradigms that caused experiencing short-term and imagining long-term exclusion. Ambiguous facial emotions were used as socio-emotional cues. In study 1, the Ostracism Online paradigm was used to manipulate short-term exclusion. In study 2, a new sample of participants imagined long-term exclusion through the future life alone paradigm. Participants of both studies then completed a facial emotion recognition task consisting of morphed ambiguous facial emotions. By means of Point of Subjective Equivalence analyses, our results indicate that the experience of short-term exclusion hinders recognising happy facial expressions. In contrast, imagining long-term exclusion causes difficulties in recognising sad facial expressions. These findings extend the current literature, suggesting that not all social exclusion paradigms affect socio-emotional processing similarly.

Exploration of MPSO-Two-Stage Classification Optimization Model for Scene Images with Low Quality and Complex Semantics.

Currently, complex scene classification strategies are limited to high-definition image scene sets, and low-quality scene sets are overlooked. Although a few studies have focused on artificially noisy images or specific image sets, none have involved actual low-resolution scene images. Therefore, designing classification models around practicality is of paramount importance. To solve the above problems, this paper proposes a two-stage classification optimization algorithm model based on MPSO, thus achieving high-precision classification of low-quality scene images. Firstly, to verify the rationality of the proposed model, three groups of internationally recognized scene datasets were used to conduct comparative experiments with the proposed model and 21 existing methods. It was found that the proposed model performs better, especially in the 15-scene dataset, with 1.54% higher accuracy than the best existing method ResNet-ELM. Secondly, to prove the necessity of the pre-reconstruction stage of the proposed model, the same classification architecture was used to conduct comparative experiments between the proposed reconstruction method and six existing preprocessing methods on the seven self-built low-quality news scene frames. The results show that the proposed model has a higher improvement rate for outdoor scenes. Finally, to test the application potential of the proposed model in outdoor environments, an adaptive test experiment was conducted on the two self-built scene sets affected by lighting and weather. The results indicate that the proposed model is suitable for weather-affected scene classification, with an average accuracy improvement of 1.42%.

The Emotional Aftermath of Surviving an Attempted Intimate Partner Homicide.

While the issue of intimate partner homicide (IPH) has gained increasing focus, research that pinpoints the experiences of women who survived an attempted IPH is limited. Specifically, studies that aim to understand the aftermath of surviving such incidents are scarce. Thus, the aim of the present study was to explore the emotional experience of IPH survivors following the attack. An interpretive phenomenological analysis was used to analyze the narratives of 11 women who had survived an attempted homicide by their partner. Four major themes emerged: Living between dichotomies: A fragmented identity; Embodied fear: A fear that will not go away; The loss of future: A life divided; and The loneliness of surviving the "unsurvivable." Utilizing the ambiguous loss theory to examine the emotional ramifications of IPH indicates that survivors navigate persistent confusion and struggle to comprehend the loss. This involves challenges in moving forward and achieving resolution, conflicting emotions related to the loss, minimal recognition of the grief, and limited support from the social environment.

How adult children of incarcerated parents experience ambiguous loss.

Families can experience grief when they lose a loved one to incarceration. Although there has not been a death, the removal of a family member from day-to-day life and the uncertainty and stigma surrounding incarceration pose major challenges. We applied consensual qualitative research methods to understand the unique grief experience that adult children have when a parent is incarcerated. Our findings elaborate on the impacts of the loss, the complicating factors of stigma and disenfranchisement, as well as how individuals have made meaning and pursued healing from this experience over time. Impacts included changes to member roles within the new family structure and difficulty forming secure bonds with peers. Participants characterized stigma toward their parent as extending to themselves and complicating their ability to openly miss their parent or process complicated reactions to the incarceration. Despite systemic challenges, participants set their personal life goals and used a combination of problem-focused coping and distancing themselves from the incarceration to successfully manage the loss. Consistent with these findings, mental health professionals serving this population can validate incarceration as a loss, repair ambiguity in family roles, develop an accepting therapeutic relationship that reduces perceived stigma, and identify possibilities for activism.

Clinically diverse and perinatally lethal syndromes with urorectal septum malformation sequence.

Urorectal septum malformation sequence (URSMS) is characterized by a spectrum of anomalies of the urogenital system, hindgut and perineum. It is presumed to be a constellation of an embryonic defect. Herein, we analyzed the clinically diverse syndromes associated with URSMS in our perinatal evaluation unit. We reviewed fetuses with URSMS in referrals for perinatal autopsy over a period of 3 years. Chromosomal microarray and genome sequencing were performed whenever feasible. Literature was reviewed for syndromes or malformations with URSMS. We ascertained URSMS in 12 of the 215 (5%) fetuses. Nine fetuses (75%) had complete URSMS and remainder had partial/intermediate URSMS. Eleven fetuses had malformations of other systems that included: cerebral ventriculomegaly; right aortic arch with double outlet right ventricle; microcephaly with fetal akinesia deformation sequence; ventricular septal defect and radial ray anomaly; thoraco-abdominoschisis and limb defects; myelomeningocele; spina bifida and fused iliac bones; omphalocele; occipital encephalocele; lower limb amelia and cleft foot. We report on six fetuses with recurrent and five fetuses with unique malformations/patterns where URSMS is a component. Exome sequencing (one family) and genome sequencing (eight families) were performed and were nondiagnostic. Additionally, we review the literature for genetic basis of this condition. URMS is a clinically heterogeneous condition and is a component of several multiple malformation syndromes. We describe several unique and recurrent malformations associated with URSMS.

Ambiguous genitalia, giant congenital melanocytic nevus and subpulmonic outlet ventricular septal defect in an African child with Neurofibromatosis 1.

Neurofibromatosis type 1 is an autosomal dominant multisystemic disease caused by mutation of the neurofibromin (NF1) gene located on chromosome 17q11. We report a case of Neurofibromatosis 1 with ambiguous genitalia, giant congenital melanocytic nevus, and associated subpulmonic outlet ventricular septal defect, hitherto unreported in sub-Saharan Africa. In addition, a literature review of congenital heart diseases associated with Neurofibromatosis 1 is presented.

The rights of migrants to the identification of their dead: an attempt at an identification strategy from Italy.

Europe is turning a blind eye on a humanitarian disaster unfolding at its doorsteps, with thousands of migrants dying unidentified in Mediterranean waters. Since 2014, Italy has been struggling in an almost indifferent international scenario to identify its dead migrants. Despite the lack of sufficient resources, of the difficulties in collecting post mortem data from the disseminated bodies, and of the problems of contacting and collecting ante mortem information from relatives, it has been proven, with a series of pilot studies, that not only can these bodies be identified but that relatives are also looking for their loved ones and need death certificates. This article focuses on the administrative limbo and lack of regulations obliging single states to engage in appropriate procedures to maximise identification.

Hemispheric functional asymmetries and sex effects in visual bistable perception.

This study investigates bistable perception as a function of the presentation side of the ambiguous figures and of participants' sex, to evaluate left-right hemispheric (LH-RH) asymmetries related to consciousness. In two experiments using the divided visual field paradigm, two Rubin's vase-faces figures were projected simultaneously and continuously 180 s long to the left (LVF) and right (RVF; Experiment 1) or to the upper (UVF) and lower (DVF; Experiment 2) visual hemifields of 48 healthy subjects monitored with eye-tracker. Experiment 1 enables stimulus segregation from the LVF to the RH and from the RVF to the LH, whereas Experiment 2 does not. Results from Experiment 1 show that males perceived the face profiles for more time in the LVF than in the RVF, with an opposite trend for the vase, whereas females show a similar pattern of perception in the two hemifields. A related result confirmed the previously reported possibility to have simultaneously two different percepts (qualia) in the two hemifields elicited by the two identic ambiguous stimuli, which was here observed to occur more frequently in males. Similar effects were not observed in Experiment 2. These findings suggest that the percepts display the processing abilities of the hemisphere currently processing the stimulus eliciting them (e.g., RH-faces), and that females and males reflect in bistable perception, a genuine manifestation of consciousness, the well-known hemispheric asymmetry differences they show in ordinary perception.

The Development of Normal Fetal External Genitalia Throughout Gestation.

In this review, we describe normal development of fetal genitalia throughout gestation as well as the identification of normal male and female genitalia on ultrasound. We use abnormal and ambiguous genitalia as illustrative tools to assist with the identification of normal genitalia and recognition of some of the most common abnormalities in external genitalia development.

Behavioral Apophenia and Dimensions of Psychoticism in Adolescents with and without Mood Disorders.

Apophenia is the tendency to falsely detect meaningful relationships and may indicate susceptibility to more extreme expressions on the psychotic spectrum. This pilot investigated the fragmented ambiguous object task (FAOT), a new measure designed to assess apophenia behaviorally in a sample of adolescents with and without mood disorders using an image recognition task. Our primary hypothesis was that increased image recognition would be associated with PID-5 psychoticism. Participants were 33 (79% female) adolescents with (n = 18) and without (n = 15) mood disorders. Consistent with predictions, increased recognition of ambiguous images correlated positively with psychoticism. There was also moderate evidence for long-term stability of FAOT apophenia scores over time (mean interval of approximately 10 months). These findings offer preliminary evidence that the FAOT may be reflective of underlying psychoticism in our target population.

Multi-Branch Attention Learning for Bone Age Assessment with Ambiguous Label.

Bone age assessment (BAA) is a typical clinical technique for diagnosing endocrine and metabolic diseases in children's development. Existing deep learning-based automatic BAA models are trained on the Radiological Society of North America dataset (RSNA) from Western populations. However, due to the difference in developmental process and BAA standards between Eastern and Western children, these models cannot be applied to bone age prediction in Eastern populations. To address this issue, this paper collects a bone age dataset based on the East Asian populations for model training. Nevertheless, it is laborious and difficult to obtain enough X-ray images with accurate labels. In this paper, we employ ambiguous labels from radiology reports and transform them into Gaussian distribution labels of different amplitudes. Furthermore, we propose multi-branch attention learning with ambiguous labels network (MAAL-Net). MAAL-Net consists of a hand object location module and an attention part extraction module to discover the informative regions of interest (ROIs) based only on image-level labels. Extensive experiments on both the RSNA dataset and the China Bone Age (CNBA) dataset demonstrate that our method achieves competitive results with the state-of-the-arts, and performs on par with experienced physicians in children's BAA tasks.

I can still hear my baby crying: The ambiguous loss of American Indian/Alaska Native birthmothers.

This study captures the experiences of American Indian/Alaska Native birthmothers who lost a child to adoption and the impact of said loss on their health and wellbeing. Few studies examine the loss experiences of American Indian/Alaska Native birthmothers despite their increased probability to lose a child to foster care and adoption. American Indian/Alaska Native birthmothers are distinct from birthmothers of other races in their experiences of intergenerational and historical child loss, having disproportionately lost their children to systematic practices of child removal via boarding schools, the adoption era, and child welfare. Interview data from 8 American Indian/Alaska Native birthmothers were analyzed using inductive thematic analysis. Five themes emerged including: (1) the social context of losing a child to adoption for American Indian/Alaska Native birthmothers, (2) the ambiguous loss of a child to adoption, (3) grief reactions to the loss, (4) the impact of the loss on birthmother health and wellbeing, and (5) creating resiliency. Findings suggest that American Indian/Alaska Native birthmothers experience ambiguous loss, as well as elevated mental health problems and substance abuse following the loss of a child to adoption.