Miracle-dz/UniFAR-FTUs huggingface dataset:
nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. Availability and implementation nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow). Visual abstract
Boundary Guided Mixing Trajectory for Semantic Control with Diffusion Models

Applying powerful generative denoising diffusion models (DDMs) for downstream tasks such as image semantic editing usually requires either ﬁne-tuning pre-trained DDMs or learning auxiliary editing networks. In this work, we achieve SOTA semantic control performance on various application settings by optimizing the denoising trajectory solely via frozen DDMs. As one of the ﬁrst optimization-based diffusion editing work, we start by seeking a more comprehensive understanding of the intermediate high-dimensional latent spaces by theoretically and empirically analyzing their probabilistic and geometric behaviors in the Markov chain. We then propose to further explore the critical step in the denoising trajectory that characterizes the convergence of a pre-trained DDM. Last but not least, we further present our method to search for the semantic subspaces boundaries for controllable manipulation, by guiding the denoising trajectory towards the targeted boundary at the critical convergent step. We conduct extensive experiments on various DPMs architectures (DDPM, iDDPM) and datasets (CelebA, CelebA-HQ, LSUN-church, LSUN-bedroom, AFHQ-dog) with different resolutions (64, 256) as empirical demonstrations. Code will be available at https://github.com/L-YeZhu/BoundaryDiffusion.
In Vitro Rigidity Effect on Breast Cancer MCF-7 Three- Dimensional Microtissue Grown from Few Cells

Background: Biological tissues normally possess varying rigidities, changes in which may reflect transformation from normal to pathological state. Cancer cells within the tumor are influenced by the mechanical conditions of their microenvironment, which can drive cell fate. Methods: We present a new on-array methodology to mimic and control desired surrounding rigidity in vitro for three-dimensional (3D) breast cancer object formation and growth. 3D objects were generated from single cells within a hydrogel array, cultured under various mechanical conditions and measured at single-object resolution. Results: Alterations in development of 3D breast cancer microtissue under various rigidity conditions in vitro are revealed. Object growth rate, morphology and vital features are associated with the extent of environmental rigidity, the point in time at which embedding was performed and the initial number of seeded cells. Under stiffness that resembles tumor tissue, higher growth rate of breast cancer microtissue and specific “preinvasive” phenotype are evident. Hallmarks of this phenotype include loose morphology with unclear edges and massive peripheral cell spread, dispersed intrinsic structure and reduced expression of epithelial surface markers. Conclusions: Physical changes in cell environment without parallel changes in biochemical conditions affect growth and development of 3D cancer microtissue grown from individual cells in vitro. A stiffer environment supports 3D microtissue growth and its morphologic and functional diversity in comparison to regular low rigidity conditions.
Pulse therapy: Opening new vistas in treatment of pemphigus

Pemphigus is comprised of a group of life-threatening autoimmune diseases that is characterized by circulating IgG antibodies targeting several types of keratinocyte antigens. After introduction of systemic steroids, survival has improved dramatically. However, mortality and morbidity were still very high due to side effects of steroids. Pulse therapy is defined as discontinuous/intermittent intravenous infusion of very high doses of corticosteroids along with certain immunosuppressive agents over a short period. This therapy was introduced to minimize the side effects of conventional corticosteroid therapy. The target is to achieve a faster response and stronger efficacy and to decrease the need for long-term use of systemic corticosteroids. As a result, this therapy has gained its popularity since three decades. The purpose of this article is to review the various available pulse therapy regimens with dosage, indications and contraindications and side effects.
Aeta Indigenous Women Healers in the Philippines: Lessons and Implications

This study investigates two central research problems. These are: What are the healing practices of Aeta women? What are the implications of the healing practices of Aeta women in the academic discourse? This inquiry is important for the following reasons: (a) it focuses a reconsidered gaze and empirical lens on the healing practices of Aeta women healers as well as the lessons, insights and perspectives which may have been previously missed; (b) my research attempts not to be 'neutral' but instead be an exercise in participatory action research and as such hopefully brings a new space of decolonization by documenting Aeta women healers’ contributions in the political and academic arena; and (c) it is an original contribution to postcolonial, anti-colonial and Indigenous feminist theories particularly through its demonstration the utility of these theories in understanding the health of Indigenous peoples and global health. There are 12 Aeta women healers who participated in the Talking Circle. This study is significant in grounding both the theory and the methodology while comparatively evaluating claims calibrated against the benchmark of the actual narratives of Aeta women healers. These evaluations subsequently categorized my findings into three themes: namely, identity, agency and representation. This work is also important in illustrating the Indigenous communities’ commonalities on resistance, accommodation, evolution and devolution of social institutions and leadership through empirical example. The work also sheds light on how the members of our Circle and their communities’ experiences with outsider intrusion and imposed changes intentionally structured to dominate them as Indigenous people altered our participants and their communities. Though the reactions of the Aeta were and are unique in this adaptive process they join a growing comparative scholarly discussion on how contexts for colonization were the same or different. This dissertation therefore joins a growing comparative educational literature on the contextual variations among global experiences with colonization. This is important since Indigenous Peoples' experiences are almost always portrayed as unique or “exotic”. I can now understand through comparison that many of the processes from military to pedagogical impositions bore striking similarities across various colonial, geographical and cultural locations.
Incremental cue training: a study of lexical tone learning by non-tonal listeners

Speech perception requires sensitivity to acoustic dimensions relevant to meaningful distinctions. Training with exaggerated cues has been used to direct second language (L2) learners’ attention to dimensions relevant for segmental contrasts; here we applied similar incremental cue training to lexical tone contrasts. Two groups of native English listeners were trained, either on a fixed tonal contrast ( high-rising vs high-falling ) or with incremental stimuli, where pitch movements relevant to the rising/falling contrast were exaggerated at training outset and reduced, stepwise, to the fixed contrast level by training completion. An ABX task tested discrimination, with feedback during training. Final tonal discrimination accuracy was similar between groups, but prior learning trajectories contrasted: the Incremental group had higher initial performance, i.e., with the exaggerated contrasts, whilst the Fixed group improved gradually over training. Finally, despite contrasting training, the groups had comparable pre-test to post-test improvement on a separate untrained tonal contrast ( high-level vs mid-rising ).
Outcome of Febrile Neutropenic Patients on Granulocyte Colony Stimulating Factor in a Tertiary Care Hospital

Febrile neutropenia is a relatively frequent event in cancer patients treated with chemotherapy. In the United States, an estimated 60,000 patients a year are hospitalized for febrile neutropenia and neutropenia related infections (Cagganio et al., 2005). Our single institution data in previous two studies have shown the frequency to be ranging from 10 to 12 per month (Lal et al., 2008; Shaikh et al., 2011). Defined as “A single oral temperature ≥38.0°C for ≥1 hour with a neutrophil count of ≤ 0.5x109/L or a neutrophil count of ≤ 1x109/L which was predicted to fall below ≤ 0.5x109/L (Pettengell et al., 2011), febrile neutropenia is a potentially life threatening situation and requires prompt medical intervention The availability of antibiotics have dramatically improved the outcome at the expense of increased cost (Kuderer et al., 2007) and hence
LEXICAL STRESS PERCEPTION IN INDIAN ENGLISHES

We report an experiment investigating the relative weighting of acoustic cues (vowel quality, intensity, duration and f0) in lexical stress perception in Indian English (IndE), compared with Southern Standard British English (SSBE). GLMM modelling of responses shows both similarities (e.g. vowel quality was by far the most important cue for both IndE and SSBE) and differences (IndE listeners were less sensitive to all cues except duration, and made least use of f0). Differentiating IndE participants according to L1 background (Indo-Aryan vs Dravidian), however, reveals a finer-grained picture, with L1 Indo-Aryan listeners exhibiting cue hierarchy and degree of cue strength that are closer to SSBE listeners. For L1 Dravidian listeners, while vowel quality remains the most important cue, the strength of this cue, and that of intensity, are significantly lower than for L1 Indo-Aryan and SSBE listeners. At the same time, duration ranks more highly for these listeners.
Probing Neural Networks for 1 Dynamic Switches of 2 Communication Pathways 3

Dynamic communication and routing play important roles in the human brain to 11 facilitate ﬂexibility in task solving and thought processes. Here, we present a network perturbation 12 methodology that allows to investigate dynamic switching between diﬀerent network pathways 13 based on phase oﬀsets between two external oscillatory drivers. We apply this method in a 14 computational model of the human connectome with delay-coupled neural masses. To analyze 15 dynamic switching of pathways, we deﬁne four new metrics that measure dynamic network 16 response properties for pairs of stimulated nodes. Evaluating these metrics for all network 17 pathways, we found a broad spectrum of pathways with distinct dynamic properties and switching 18 behaviors. Speciﬁcally, we found that 60.1% of node pairs can switch their communication from 19 one pathway to another depending on their phase oﬀsets. This indicates that phase oﬀsets and 20 coupling delays play an important computational role for the dynamic switching between 21 communication pathways in the brain. 22
The influence of tone experience and native tone and intonation categories on nonnative tone learning

For many languages, lexical tone is a linguistic feature which assigns meaning to words through variations in pitch. Learning tone as a new feature can be challenging, though training can improve learning outcomes for native tone and nontone listeners alike. Still, there is little consensus on whether native tone experience bolsters nonnative tone learning. This study examined the influence of the listener’s native language on the learning of an artificial tone language. After five training sessions, nontonal Australian English, tonal Mandarin, and tonal Vietnamese listeners showed improvements in tone identification and word learning. Tone language listeners demonstrated greater performance in word learning, and Mandarin listeners outperformed the other groups in tone identification. Further investigation of tone identification patterns showed some tones were easier to perceive for all groups, though performance was also influenced by how closely the tones were mapped onto the listeners’ native tone and intonation categories.
Cue weighting in Mandarin tone perception: A comparison between native speakers and learners of Mandarin

Some studies have shown that advanced learners of Mandarin perceive Mandarin tones more categorically compared to non-native speakers without prior experience. However, these studies have mainly focused on one single cue. In the current study, the author investigated the interaction between two acoustic-phonetic cues (turning point position (TP) and f0 at the end (End f0)) during perception between Tone 2 and Tone 3 and how English listeners of Mandarin adapt their perceptual strategies to distinguish categories that do not exist in their L1. The results show that native Mandarin listeners tend to use a TP-dominant strategy, whereas non-native listeners rely less on TP. No significant difference was found in cue weighting between the learners and naïve English listeners. We suggest that native Mandarin listeners are able to exploit TP to filter out the uncritical portion, whereas learners of Mandarin focus more on the canonical textbook forms of Mandarin tones.
VOWEL SPACE AREA CHANGES IN CHILDREN WITH DYSARTHRIA

Increasing speech intelligibility is an essential treatment target for children with dysarthria secondary to cerebral palsy. Vowel space area (VSA) is associated with intelligibility in dysarthria. The speech cues “speak with your big mouth” and “speak with your strong voice” have been found to increase intelligibility in this population. This study examined changes in VSA in response to speech cues in children with dysarthria. We further investigated whether dysarthria severity impacted the VSA changes. Thirteen children with dysarthria were cued to speak with a “big mouth” or “strong voice. ” First and second formants were measured from four corner vowels in carrier sentences. Preliminary results show a trend toward increased VSA, with children with mild dysarthria exhibiting the greatest changes. Therefore, cueing children with dysarthria, especially mild dysarthria, to speak with their “big mouth” and/or “strong voice” may increase their VSA and thus, potentially contribute to increasing their intelligibility.
THE EFFECT OF SPEAKER ON SPEECH INTELLIGIBILITY

Most perception and intelligibility studies assume that noise masks spoken-sentence stimuli equivalently regardless of the speaker. That is, any sentence is equally intelligible across speakers when controlled for style and rate. However, previous studies have shown significant intelligibility variation between speakers. In this study, we predict speaker-specific intelligibility differences in noise for 720 IEEE/Harvard sentences produced by 20 Pacific Northwest speakers (10 women and 10 men). In this corpus, style and rate are controlled in the productions to avoid clear speech. Each sentence recording ( n = 14 , 400 ) was mixed with corpus-shaped noise at three levels (+2, 0, -2 dB) resulting in 43,200 total stimuli. Sentence intelligibility was calculated from orthographic transcriptions provided by 1,868 English-speaking listeners to 120 randomly selected stimuli presented online. We find that different speakers have different intrinsic intelligibility even when reading the same set of sentences. Moreover, some speakers’ speech was more affected by noise than others.
Patient and Professional factors that impact the perceived likelihood and confidence of healthcare professionals to discuss Implantable Cardioverter Defibrillator deactivation in advanced heart failure: Results from an International Factorial Survey

Background: Rate of implantable cardioverter defibrillator (ICD) implantations is increasing in patients with advanced heart failure. Despite clear guideline recommendations, discussions addressing deactivation occur infrequently. Aim: The aim of this article is to explore patient and professional factors that impact perceived likelihood and confidence of healthcare professionals to discuss ICD deactivation. Methods and Results: Between 2015 and 2016, an international sample of 262 healthcare professionals (65% nursing, 24% medical) completed an online factorial survey, encompassing a demographic questionnaire and clinical vignettes. Each vignette had 9 randomly manipulated and embedded patient-related factors, considered as independent variables, providing 1572 unique vignettes for analysis. These factors were determined through synthesis of a systematic literature review, a retrospective case note review, and a qualitative exploratory study. Results showed that most healthcare professionals agreed that deactivation discussions should be initiated by a cardiologist (95%, n = 255) or a specialist nurse (81%, n = 215). In terms of experience, 84% of cardiologists (n = 53) but only 30% of nurses (n = 50) had previously been involved in a deactivationdecision.Healthcareprofessionals valuedpatientinvolvementindeactivationdecisions; however, only50% (n = 130) actively involved family members. Five of 9 clinical factors were associated with an increased likelihood to discussdeactivationincludingadvancedage,severeheartfailure,presenceofmalignancy,receiptofmultipleICDshocks, and more than 3 hospital admissions during the previous year. Furthermore, nationality and discipline significantly influenced likelihood and confidence in decision making. Conclusions: Guidelines recommend that healthcare professionals discuss ICD deactivation; however, practice is suboptimal with multifactorial factors impacting on decision making. The role and responsibility of nurses in discussing deactivation require clarity and improvement.
PRENASALIZATION IN GREEK-LEARNING CHILDREN WITH COCHLEAR IMPLANTS AND TYPICAL HEARING

This work compares nasalance measures for word-initial consonants in Greek-learning children with typical hearing and with cochlear implants [CIs]. An interesting feature of Greek is that many dialects employ prenasalization of phonemically voiced stops. One can anticipate that the rapid shift between an open vs. closed velopharyngeal port represents a challenge to typical children, and all the more so for those who do not have typical hearing. Greek-speaking children with CIs have been found to have longer prevoicing, which could reflect greater nasal coupling. Current results show that children with CIs, compared to those with NH, have a lower proportion of prevoicing; higher nasalance values for the consonant, vowel, and word; and greater variability in nasalance measures for the consonant, vowel, and word. Some children with CIs showed considerable carryover nasalization from the initial stop consonant. Despite these group-level patterns, speaker-specific variation is extensive in both groups.
Hydraulic conductivity of bedding-parallel cracks in shale as a function of shear and normal stress

Abstract Conductivity of fluids along fractures in all rocks is reduced by increasing normal stress. For sandstones and other hard rocks the onset of shear failure along planar cracks is thought to enhance fluid flow owing to a small amount of dilatancy, yet such effects are poorly quantified. Here we determine experimentally how independently increasing normal and shear stress affects fluid flow along fractures in shale. Gas flow along bedding-parallel planar interfaces was measured for flow parallel and normal to the shear direction. Increasing shear stress causes accelerating reduction of conductivity, even before the onset of macroscopic slip. Such reduction in fluid flow rate is non-recoverable, and the combined effects of normal and shear stress can reduce fracture conductivity by more than 3 orders of magnitude over the range of shale reservoir conditions. Bedding plane-parallel slip is common in shales; it can result in a large enhancement of permeability anisotropy, because flow across bedding planes becomes inhibited. This can impact upon the geometry of developing hydraulic fractures, encouraging complexity and favouring lateral relative to vertical growth. The results will facilitate modelling of fluid flow through fracture networks. Supplementary material: A CSV file containing all experimental conditions and tabulations of results is available at https://doi.org/10.6084/m9.figshare. c.3721831.
SPECTRAL CUES IN PITCH PERCEPTION IN ENGLISH AND CANTONESE SPEECH AND MUSIC

Listeners integrate multidimensional cues (e.g., spectral shape) during pitch processing in both speech and music. While prior works have shown that this effect applies to tonal and non-tonal speakers, it remains unclear whether listeners’ pitch processing strategies differ on different linguistic levels (e.g. tone vs intonation). Furthermore, work has yet to show whether differences in pitch processing lie between natural (both speech and music) vs artificial sounds, or speech vs non-speech sounds. A pitch classification experiment investigated these questions. Listeners were either English or Cantonese speakers listening to stimuli modeled after Cantonese prosody, or English speakers listening to comparable violin stimuli. Results show that all participants integrate spectral cues in pitch perception. However, the effect of musicality on shift but not categoricity differed between Cantonese and English speech conditions. Overall results suggest shared pitch processing for speech and music.