Miracle-dz/UniFAR-FTUs huggingface dataset:
The Argo: A 65,536 channel recording system for high density neural recording in vivo

Here we demonstrate the Argo System, a massively parallel neural recording system based on platinum-iridium microwire electrode arrays bonded to a CMOS voltage amplifier array. The Argo system is the highest channel count in vivo neural recording system built to date, supporting simultaneous recording from 65,536 channels, sampled at over 32 kHz and 12-bit resolution. This system is designed for cortical recordings, compatible with both penetrating and surface microelectrodes. We have validated this system by recording spiking activity from 791 neurons in rats and cortical surface Local Field Potential (LFP) activity from over 30,000 channels in sheep. While currently adapted for head-fixed recording, the microwire-CMOS architecture is well suited for clinical translation. Thus, this demonstration helps pave the way for a future high data rate intracortical implant.
A theoretical model of neural maturation in the developing spinal cord

Cellular differentiation is a tightly regulated process under the control of intricate signaling and transcription factors networks working in coordination. Due to their complexity, these networks are studied and modelled independently despite their codependence: signals instruct transcription factors to drive cellular responses, and transcription factors provide the context for the cells to respond to signals. These reciprocal interactions make the systems dynamic, robust and stable but also difficult to dissect. Differential equation based mathematical models provide an important theoretical tool to understand the behavior of these intricate networks. In the spinal cord, recent work has shown that a network of FGF, Wnt and Retinoic Acid (RA) signaling factors regulate neural maturation by directing the activity of a transcription factor network that contains CDX at its core. Here we have used differential equation based models to understand the spatiotemporal dynamics of the FGF/Wnt/RA and the CDX regulated networks, alone and in combination. We show that in both networks, the strength of interaction among network partners impacts the dynamics, behavior and output of the system. In the signaling network, small changes in the strength of the interactions among networking partners can result in a signal overriding, balancing or oscillating with another signal. We also show that the signaling network conveys the spatiotemporal information to the transcription network, whose interpretation produces a transition zone to separate regions of high cell potency from regions of cell differentiation. This analysis provides a model for the interaction conditions underlying spinal cord cell maturation during embryonic axial elongation.
Evaluation of a fine-mapping method exploiting linkage disequilibrium in livestock populations : Simulation study

A simulation study was conducted to evaluate a fine-mapping method exploiting population-wide linkage disequilibrium. Data were simulated according to the pedigree structure based on a large paternal half-sib family population with a total of 1,034 or 2,068 progeny. Twenty autosomes of 100 cM were generated with 5 cM or 1 cM marker intervals for all founder individuals in the pedigree, and marker alleles and a number of quantitative trait loci (QTL) explaining a total of 70% phenotypic variance were generated and randomly assigned across the whole chromosomes, assuming linkage equilibrium between the markers. The founder chromosomes were then descended through the pedigree to the current offspring generation, including recombinants that were generated by recombination between adjacent markers. Power to detect QTL was high for the QTL with at least moderate size, which was more pronounced with larger sample size and denser marker map. However, sample size contributed much more significantly to power to detect QTL than map density to the precise estimate of QTL position. No QTL was detected on the test chromosomes in which QTL was not assigned, which did not allow detection of false positive QTL. For the multiple QTL that were closely located, the estimates of the QTL positions were biased, except when the QTL were located on the right marker positions. Our fine mapping simulation results
Genetic control of Schwann cell differentiation

textabstractSchwann cellen myelineren axonen onder de invloed van axonale signalen. Het is nog niet volkomen duidelijk welke signalen dat zijn. Ondanks dat zijn er de laatste jaren wel veel intracellulaire regulatoren van het myelinatie programma geA¯dentificeerd en bestudeerd. Verschillende factoren die een rol spelen tijdens de ontwikkeling van de myelinerende Schwann cel worden in dit proefschrift beschreven. Twee van de belangrijkste factoren zijn Oct-6 en Krox-20. Wanneer een van beide factoren afwezig is tijdens de ontwikkeling dan vindt er geen myelinatie plaats in de Krox-20 knock-out muis en in de Oct-6 knock-out muis uiteindelijk wel, maar met een flinke vertraging. Omdat er in de Oct-6 mutant uiteindelijk alsnog myelinatie plaatsvindt is er gezocht naar eventuele ander factoren die daar verantwoordelijk voor zouden kunnen zijn. Het blijkt nu als Brn-2 samen met Oct-6 afwezig is tijdens de ontwikkeling van de zenuwen dat dan ook in dit geval geen myelinatie meer optreedt. Wanneer nu overexpressie van Brn-2 in de Oct-6 mutant tot stand wordt gebracht blijkt dat myelinatie van de axonen op bijna het normale niveau plaats vindt. Naast deze Oct-6 en Krox-20 mutanten is er ook nog een natuurlijke mutant clawpaw. Deze mutant vertoont net als de Oct-6 mutant een ernstige vertraging in de myelinatie van de axonen. De natuurlijke mutant clawpaw heeft een afwijkende Lgi4 expressie. Dit kan een indicatie zijn dat Lgi4 betrokken is bij het myelinatie proces in de Schwann cel.
Rational Design of Antigen Incorporation Into Subunit Vaccine Biomaterials Can Enhance Antigen-Specific Immune Responses

Peptide subunit vaccines increase safety by reducing the risk of off-target responses and improving the specificity of the induced adaptive immune response. The immunogenicity of most soluble peptides, however, is often insufficient to produce robust and lasting immunity. Many biomaterials and delivery vehicles have been developed for peptide antigens to improve immune response while maintaining specificity. Peptide nanoclusters (PNC) are a subunit peptide vaccine material that has shown potential to increase immunogenicity of peptide antigens. PNC are comprised only of crosslinked peptide antigen and have been synthesized from several peptide antigens as small as 8 amino acids in length. However, as with many peptide vaccine biomaterials, synthesis requires adding residues to the peptide and/or engaging amino acids within the antigen epitope covalently to form a stable material. The impact of antigen modifications made to enable biomaterial incorporation or formation is rarely investigated, since the goal of most studies is to compare the soluble antigen with biomaterial form of antigen. This study investigates PNC as a platform vaccine biomaterial to evaluate how peptide modification and biomaterial formation with different crosslinking chemistries affect epitope-specific immune cell presentation and activation. Several types of PNC were synthesized by desolvation from the model peptide epitope SIINFEKL, which is derived from the immunogenic protein ovalbumin. SIINFEKL was altered to include extra residues on each end, strategically chosen to enable multiple conjugation chemistry options for incorporation into PNC. Several crosslinking methods were used to control which functional groups were used to stabilize the PNC, as well as the reducibility of the crosslinking. These variations were evaluated for immune responses and biodistribution following in vivo immunization. All modified antigen formulations still induced comparable immune responses when incorporated into PNC compared to unmodified soluble antigen alone. However, some crosslinking methods led to a significant increase in desirable immune responses while others did not, suggesting that not all PNC were processed the same. These results help guide future peptide vaccine biomaterial design, including PNC and a wide variety of conjugated and self-assembled peptide antigen materials, to maximize and tune the desired immune response.
Aberrant Resting-State Brain Function in Adolescent Depression

To explore the changes of brain function and conduct clinical differential diagnosis based on support vector machine (SVM) in adolescent patients with depression. A total of 24 adolescent patients with depression according to CCMD-3 and DSM-5 and 23 gender, education level, body mass index, and age matched healthy controls were assessed with 17-item Hamilton Depression Rating Scale (HAMD). HAMD scores were requested from ≥17 of patients. Three−dimensional T1 and resting-state functional magnetic resonance imaging data were acquired from all participants. The data were analyzed using SPM 12 and REST1.8. Two-sample t-test was conducted to compare regional homogeneity (ReHo) values among the groups of participants. Finally, based on SVM classification, clinical differential diagnosis of the patients was carried out. The receiver operator characteristic (ROC) curve were used to confirm the performance of the SVM model. An increase ReHo values were observed in the lingual gyrus, middle occipital gyrus, postcentral gyrus, and precentral gyrus, whereas a decrease in ReHo was found in vermis compared with the control group. The SVM model showed good performance in classification prediction of adolescent depression, with an area under curve (AUC) of 0.778 [95% confidence interval (CI), 0.661–0.797]. The changes in the spontaneous neural activity of these regions may play an important role in the neuropathological mechanism of adolescent depression and may provide promising markers for clinical evaluation.
ZnO Nanomaterials: Current Advancements in Antibacterial Mechanisms and Applications

The prevalence of various diseases caused by bacteria has been increasing, and some traditional antibiotics have been reported to have varying degrees of resistance. ZnO nanomaterials (ZnO-NMs), due to their excellent broad-spectrum antibacterial properties, lasting antibacterial effects, and excellent biocompatibility, have quickly become the research focus of new antibacterial agents. While the narrow light response range of ZnO-NMs has limited the antibacterial performance to some extent and modifying it by various means to improve its response under visible light, such as doping metal/non-metal atoms, depositing noble metals and coupling carbon materials, which is a new research hotspot. Herein, the current mainstream claims about the antibacterial mechanisms and applications of ZnO-NMs are reviewed.
BROILER PERFORMANCE IN RESPONSE TO PHYTATE AND SUPPLEMENTED PHYTASE

Phosphorus (P) is a macro mineral in broiler nutrition. In growing broilers, besides its requirement for proper bone development, it is also involved in almost all metabolic processes. Poor P availability results in decreased productivity and poor health status.Phosphorus availability from plant derived feeds is affected by an anti-nutritional factor “phytate”, which forms a variety of insoluble salts with most of the minerals including P, calcium (Ca), magnesium, zinc (Zn) and copper (Cu) due to its reactive anion capability. So, phytate is responsible for considerable nutrient losses as vegetable sources form a major portion in broiler diet formulations. Phytate has also been reported to form complexes with protein and proteolytic enzymes (pepsin and trypsin). Mono-gastric animals lack endogenous phytase (an enzyme capable of hydrolyzing phytate bound P, Ca, protein and other nutrients), so phytate decreases the nutrient availability at the intestinal level in poultry. Application of phytase in poultry rations may liberate cations and other nutrients bound by phytate-P complexes resulting in improved production parameters and body structure characteristics in broilers. However, efficacy of supplemental phytase rests on its rate of application, Ca: P in ration, composition of diet, genotype and age of birds. Phytase could ensure the economical poultry production by the exploitation of inherent nutritional potential of feedstuffs. Some studies, however, showed that phytase does not degrade dietary phytate efficiently and thus the negative influence of phytate on protein digestibility is not completely removed by phytase supplementation. More focused researchon currently available phytase feed enzymes and their potentialimproved action by the simultaneous use of other exogenous enzymes, which complement their activity is recommended.
A Closer Look at Anandamide Interaction With TRPV1

The transient receptor potential subfamily vanilloid type 1 ion channel (TRPV1), located in the peripheral nervous system has been implicated in the perception of pain and possesses the ability to be modulated by various cannabinoid ligands. Because of its location, TRPV1 is an ideal target for the development of novel pain therapeutics. Literature precedent suggests a wide range of cannabinoid ligands can activate TRPV1, but the location and mode of entry is not well understood. Understanding the modes in which cannabinoids can enter and bind to TRPV1 can aid in rational drug design. The first endogenous ligand identified for TRPV1 was the endocannabinoid, anandamide (AEA). The Molecular Dynamics (MD) studies discussed here investigate the entry mode of AEA into TRPV1. During the course of the 10+ microsecond MD simulations, two distinct binding modes were observed: AEA binding in the tunnel formed by the S1–S4 region, and AEA binding in the vanilloid binding pocket, with preference for the former. Unbiased MD simulations have revealed multiple spontaneous binding events into the S1–S4 region, with only one event of AEA binding the vanilloid binding pocket. These results suggest that AEA enters TRPV1 via a novel location between helices S1–S4 via the lipid bilayer.
Frequency of Breast Cancer Surgery Related Arm Lymphedema at King Abdulaziz University Hospital 2008 – 2015, a Tertiary Center Experience, Jeddah, Saudi Arabia

The purpose of this retrospective study was to investigate the frequency of breast cancer-related lymphedema at King Abdulaziz University Hospital and factors associated with it. Eighty-four breast cancer-related lymphedema patients were recruited from Plastic and Reconstruction Surgery Unit, King Abdulaziz University Hospital, Jeddah, Saudi Arabia after breast cancer treatment during the period from 2008 till 2015. According to the circumference difference between healthy and affected arm, lymphedema degree was categorized into mild (> 5-10%), moderate (> 10-15%) and severe (> 15%). From a total of 598 patients who underwent breast cancer resection, 84 (14.05%) patients developed breast cancer-related lymphedema. In out of the 84 patients who developed arm lymphedema, the treatment was mostly modified radical mastectomy and radiotherapy (n = 59, 70.24%); followed by lumpectomy plus axillary lymph node dissection and radiotherapy (n = 18, 21.43%), simple mastectomy (n = 5, 5.95%) and lumpectomy with sentinel lymph node dissection and radiotherapy (n = 2, 2.38%) with statistical significant difference between them (P = 0.0001). The frequency of lymphedema in our institution is 14.05%. It is mostly moderate, appears during the 1st year after surgery in patients who underwent modified radical mastectomy and radiotherapy, aged more than 60 years and obese.
Chronology and Geomorphological Activity of the Akdag Rock Avalanche (SW Turkey)

Large rock-slope failures are among the primary geohazards in high mountain areas. These rock avalanches and rockslides constitute most of the world’s largest landslide deposits. This study focuses on the formation and geomorphological activity of the Akdag landslide complex located on the southern slope of Mount Akdag, SW Turkey. We employed detailed mapping in the field, spatial and morphometric analysis using GIS and remote sensing technologies, and surface exposure dating with cosmogenic 36Cl to reconstruct the chronology of the landslide complex. For the analysis of cosmogenic 36Cl, we collected 18 surface samples from calcareous boulders within the landslide deposit. Our field mapping shows that the Akdag rock avalanche is a large and active slope failure developed between carbonates and flysch. The rock-avalanche deposits cover an area of 9.8 km2 and together with the primary and secondary slope failures which form the landslide complex, cover an area of 15 km2. The Akdag rock avalanche is one of the largest (3 × 108 m3) known bedrock landslides in Turkey. Cosmogenic 36Cl exposure ages indicate that the main collapse occurred at 8.3 ± 1.4 ka (2σ), followed by secondary failures. We dated one of the latter to 1.1 ± 0.2 ka (2σ). Based on field evidence, we surmise that increased water discharge in the springs along the carbonate-flysch contact zone played a key role in the Early Holocene failure.
Comparison of Hematologic Toxicity and Bone Marrow Compensatory Response in Head and Neck vs. Cervical Cancer Patients Undergoing Chemoradiotherapy

Background: Hematologic toxicity is a critical problem limiting treatment delivery in cancer patients undergoing concurrent chemoradiotherapy. However, the extent to which anatomic variations in radiation dose limit chemotherapy delivery is poorly understood. A unique natural experiment arises in patients with head and neck and cervical cancer, who frequently undergo identical chemotherapy but receive radiation to different regions of the body. Comparing these cohorts can help elucidate to what extent hematologic toxicity is attributable to marrow radiation as opposed to chemotherapy. Methods: In this longitudinal cohort study, we compared hematologic toxicity and bone marrow compensatory response in 148 patients (90 cervix, 58 head/neck) undergoing chemoradiotherapy with concurrent weekly cisplatin 40 mg/m2. We used linear mixed effect models to compare baseline and time-varying peripheral cell counts and hemoglobin levels between cohorts. To assess bone marrow compensatory response, we measured the change in metabolically active bone marrow (ABM) volume on 18F-fluorodeoxyglucose positron emission tomography/computed tomography. Results: We observed greater reductions in log-transformed lymphocyte, platelet, and absolute neutrophil counts (ANC) for cervix compared to head/neck cancer patients (fixed effects for time-cohort interaction [95% CI]: lymphocytes, −0.06 [−0.09, −0.031]; platelets,−0.028 [-0.051, −0.0047]; ANC, −0.043 [−0.075, −0.011]). Mean ANC nadirs were also lower for cervical vs. head/neck cancer cohorts (2.20 vs. 2.85 × 103 per μL, p < 0.01). Both cohorts exhibited reductions in ABM volume within the radiation field, and increases in ABM volume in out-of-field areas, indicating varying compensatory response to radiation injury. Conclusions: Cervical cancer patients had faster decreases in ANC, lymphocyte, and platelet counts, and lower ANC nadirs, indicating a significant effect of pelvic irradiation on acute peripheral blood cell counts. Both cohorts exhibited a compensatory response with increased out-of-field bone marrow activity.
Youth and Food Systems Transformation

What, if anything, is special about youth with respect to engagement in food systems? This question is important, owing to the size of the current demographic cohort of youth, globally but especially in the majority world, as well as the large stake, and strong influence, that today's youth will have in the development trajectories and future sustainability of food systems. Although youth is often framed as an age category for policy and bureaucratic purposes, this simplification obscures important dimensions of what being a youth means and entails. It makes comparisons and generalizations simple but misleading, because age-based classifications are nationally and culturally specific. In this paper, we argue that youth is better understood relationally, as a transitional phase within the life course. While every human being depends on consuming food, their individual transition from childhood to adulthood involves—as a very stylized generalization—a significant enlargement of autonomy and independence, as well as an increased likelihood of being substantially and directly involved in the production, distribution, procurement and/or preparation of food, as well as its consumption. However, each person's youth transition and their relationship with food systems is uniquely shaped by specific intersections with multiple factors including gender, class, wealth, health, location, intergenerational relationships, and many others. We conclude that there are only a few, important but not necessarily dominant, ways in which youth as a group have special stakes in food systems. We elaborate on this complex picture and identify some principles to guide development research and policy that seeks to engage with youth in relation to the sustainable transformation of food systems.
Drainage and Elevation as Factors in the Restoration of Salt Marsh in Britain

Intertidal restoration through realignment of flood defenses has become an important component of the U.K. coastal and estuarine management strategy. Although experimentation with recent deliberate breaches is in progress, the long‐term prognosis for salt marsh restoration can be investigated at a number of sites around Essex, southeast England where salt marshes have been reactivated (unmanaged restoration) by storm events over past centuries. These historically reactivated marshes possess higher creek densities than their natural marsh counterparts. Both geomorphology and sedimentology determine the hydrology of natural and restored salt marshes. Elevation relative to the tidal frame is known to be the primary determinant of vegetation colonization and succession. Yet vegetation surveys and geotechnical analysis at a natural marsh, where areas with good drainage exist in close proximity to areas of locally hindered drainage at the same elevation, revealed a significant inverse relationship between water saturation in the root zone and the abundance of Atriplex portulacoides, normally the physiognomic dominant on upper salt marsh in the region. Elsewhere in Essex natural and restored marshes are typified by very high sediment water contents, and this is reflected in low abundance of A. portulacoides. After a century of reestablishment no significant difference could be discerned between the vegetation composition of the storm‐reactivated marshes and their natural marsh counterparts. We conclude that vegetation composition may be restored within a century of dike breaching, but this vegetation does not provide a reliable indicator of ecological functions related to creek structure.
Entities with Quantities

Unstructured content, like text in web pages, and semistructured content, like HTML tables in web pages, has much weaker search functionality compared to structured databases. For example, joins between text documents via co-occurring entity mentions or attribute values are infeasible, unless major efforts are taken to create markup for a structured view. As for web tables, filters on entity mentions allow users to look up data, but results are noisy and error-prone because of ad-hoc choices for names of entities and value encodings, with huge heterogeneity across tables and often even within a table. In the last few years, large knowledge graphs (KG), machine learning (ML) techniques and advances in entity linking algorithms [12, 17] have enabled search engines to overcome these issues, to a large degree [13]. By detecting entity mentions in web content and normalizing them onto KG entries, it has become possible to answer entity-centric queries about people, places and products almost as precisely and concisely as a database query. The following examples work with all major search engines and return crisp entity-level answers: