Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine Mapping of the Affecting Tillering and Plant Height Gene CHA-1 in Rice

The plant architecture of rice is an important factor affecting yield. Strigolactones (SLs) are newly discovered carotenoid-derived plant hormones that play an important role in rice plant architecture. In this study, a high-tillering dwarf mutant, CHA-1, was identified by spatial mutagenesis. CHA-1 was located in the region of 31.52–31.55 MB on chromosome 1 by map-based cloning. Compared with the wild-type THZ, the CHA-1 mutant showed that ACCAC replaced TGGT in the coding region of the candidate gene LOC_Os01g54810, leading to premature termination of expression. Genetic complementation experiments proved that LOC_Os01g54810 was CHA-1, which encodes a putative member of Class III lipase. Expression analysis showed that CHA-1 was constitutively expressed in various organs of rice. Compared with those in THZ, the expression levels of the D17 and D10 genes were significantly downregulated in the CHA-1 mutant. In addition, the concentrations of ent-2′-epi-5-deoxystrigol (epi-5DS) in the root exudates of the CHA-1 mutant was significantly reduced compared with that of THZ, and exogenous application of GR24 inhibited the tillering of the CHA-1 mutant. These results suggest that CHA-1 influences rice architecture by affecting SL biosynthesis.
Limited codifferential method for nonsmooth convex optimization problems

In this study, a new algorithm to minimize the convex functions is developed. This algorithm is based on the concept of codifferential. Since the computation of whole codifferential is not always possible, we use a few elements from the codifferential. When computing descent directions, fixed number elements of the codifferential are used at each iteration. The convergence of the proposed minimization algorithm is proved. In order to compare, developed method with subgradient and bundle methods, the well-known nonsmooth optimization academic test problems. We obtain numerical results for the number $l=2$, which shows us the developed method is better than subgradient methods. If the objective function is maximum of some other functions, the bundle method gives better results, however, for the other types of objective functions our method is as good as the bundle method. In our future studies, our aim is to obtain numerical results for the number $l=3$ and $l=4$. Our prediction is that the results will be better although time consumption will increase. As a conclusion, we develop a new method by using codifferential and it can be used as an alternative method because of its efficiency and robustness.
Magnetic and noncentrosymmetric Weyl fermion semimetals in the RAlX family of compounds (R=rare earth, Al=aluminium, X=Si, Ge)

Weyl semimetals are novel topological conductors that host Weyl fermions as emergent quasiparticles. While the Weyl fermions in high-energy physics are strictly defined as the massless solution of the Dirac equation and uniquely fixed by Lorentz symmetry, there is no such constraint for a topological metal in general. Specifically, the Weyl quasiparticles can arise by breaking either the space-inversion ($\mathcal{I}$) or time-reversal ($\mathcal{T}$) symmetry. They can either respect Lorentz symmetry (type-I) or strongly violate it (type-II). To date, different types of Weyl fermions have been predicted to occur only in different classes of materials. In this paper, we present a significant materials breakthrough by identifying a large class of Weyl materials in the RAlX (R=Rare earth, Al, X=Ge, Si) family that can realize all different types of emergent Weyl fermions ($\mathcal{I}$-breaking, $\mathcal{T}$-breaking, type-I or type-II), depending on a suitable choice of the rare earth elements. Specifically, RAlX can be ferromagnetic, nonmagnetic or antiferromagnetic and the electronic band topology and topological nature of the Weyl fermions can be tuned. The unparalleled tunability and the large number of compounds make the RAlX family of compounds a unique Weyl semimetal class for exploring the wide-ranging topological phenomena associated with different types of emergent Weyl fermions in transport, spectroscopic and device-based experiments.
Particle swarm optimization algorithm combination with Powell search method

In order to further improve the efficiency of multi-modal function optimization,a novel hybrid algorithm which combines improved particle swarm optimization algorithm and Powell search method is proposed.The Powell-IPSO hybrid algorithm organically integrates PSO algorithm which has powerful global search capability with Powell search method which has strong local search ability.The hybrid algorithm ensures quick convergent speed and find all extreme points as much as possible,and solution’s precision is improved.The hybrid algorithm only uses function values information and doesn’t need to calculate the derivative of function.So it is a generalized algorithm for multi-modal function of differentiable and non-differentiable.The simulation experionents show the effectiveness of the hybrid algorithm.
Metabolically Active Zones Involving Fatty Acid Elongation Delineated by DESI-MSI Correlate with Pathological and Prognostic Features of Colorectal Cancer

Colorectal cancer (CRC) is the second leading cause of cancer deaths. Despite recent advances, five-year survival rates remain largely unchanged. Desorption electrospray ionization mass spectrometry imaging (DESI) is an emerging nondestructive metabolomics-based method that retains the spatial orientation of small-molecule profiles on tissue sections, which may be validated by ‘gold standard’ histopathology. In this study, CRC samples were analyzed by DESI from 10 patients undergoing surgery at Kingston Health Sciences Center. The spatial correlation of the mass spectral profiles was compared with histopathological annotations and prognostic biomarkers. Fresh frozen sections of representative colorectal cross sections and simulated endoscopic biopsy samples containing tumour and non-neoplastic mucosa for each patient were generated and analyzed by DESI in a blinded fashion. Sections were then hematoxylin and eosin (H and E) stained, annotated by two independent pathologists, and analyzed. Using PCA/LDA-based models, DESI profiles of the cross sections and biopsies achieved 97% and 75% accuracies in identifying the presence of adenocarcinoma, using leave-one-patient-out cross validation. Among the m/z ratios exhibiting the greatest differential abundance in adenocarcinoma were a series of eight long-chain or very-long-chain fatty acids, consistent with molecular and targeted metabolomics indicators of de novo lipogenesis in CRC tissue. Sample stratification based on the presence of lympovascular invasion (LVI), a poor CRC prognostic indicator, revealed the abundance of oxidized phospholipids, suggestive of pro-apoptotic mechanisms, was increased in LVI-negative compared to LVI-positive patients. This study provides evidence of the potential clinical utility of spatially-resolved DESI profiles to enhance the information available to clinicians for CRC diagnosis and prognosis.
CONTINUED FRACTIONS AND JACOBI SYMBOLS

We consider the regular continued fraction expansion of a rational number m/N, m ≥ 0, N ≥ 1, (m, N) = 1. Let s/t, (s, t) = 1, be the kth convergent of this expansion and p/q, (p, q) = 1, be the complete quotient belonging to s/t. We give some relations for Jacobi symbols, a typical example of which is for k, t, q, N odd, with a simple right-hand side depending on t, q, N (mod 4). As an application, we prove the periodicity of the Jacobi symbol for the convergents s/t of infinite purely periodic continued fractions.
High-Risk Pedigree Study Identifies LRBA (rs62346982) as a Likely Predisposition Variant for Prostate Cancer

Simple Summary There remains a lack of identification of genes responsible for the most aggressive of prostate cancers. A unique resource consisting of sampled, related men who died from their confirmed prostate cancer and who were members of pedigrees shown to have a significant excess of prostate cancer cases has allowed the identification of multiple rare candidate predisposition variants for prostate cancer. Strong candidate variants are presented, including a rare, validated variant in the gene LRBA, all of which can be examined further in additional studies. Abstract There is evidence for contribution of inherited factors to prostate cancer, and more specifically to lethal prostate cancer, but few responsible genes/variants have been identified. We examined genetic sequence data for 51 affected cousin pairs who each died from prostate cancer and who were members of high-risk prostate cancer pedigrees in order to identify rare variants shared by the cousins as candidate predisposition variants. Candidate variants were tested for association with prostate cancer risk in UK Biobank data. Candidate variants were also assayed in 1195 additional sampled Utah prostate cancer cases. We used 3D protein structure prediction methods to analyze structural changes and provide insights into mechanisms of pathogenicity. Almost 4000 rare (<0.005) variants were identified as shared in the 51 affected cousin pairs. One candidate variant was also significantly associated with prostate cancer risk among the 840 variants with data in UK Biobank, in the gene LRBA (p = 3.2 × 10−5; OR = 2.09). The rare risk variant in LRBA was observed to segregate in five pedigrees. The overall predicted structures of the mutant protein do not show any significant overall changes upon mutation, but the mutated structure loses a helical structure for the two residues after the mutation. This unique analysis of closely related individuals with lethal prostate cancer, who were members of high-risk prostate cancer pedigrees, has identified a strong set of candidate predisposition variants which should be pursued in independent studies. Validation data for a subset of the candidates identified are presented, with strong evidence for a rare variant in LRBA.
NGC 4254: A Spiral Galaxy with an M = 1 Mode and Infalling Gas

We present high-resolution H I and Hα observations of the spiral galaxy NGC 4254. The observations were obtained with the VLA and the Maryland-Caltech Fabry-Perot camera, respectively. NGC 4254 is unusual in having a grand-design spiral structure with a strong m=1 component for which there is no obvious cause in optical images. Our observations reveal that, in addition to the usual galactic disk component, there are H I clouds superposed on and beyond the H I disk, at velocities up to 150 km s −1 from those established for the disk. The mass in these clouds is ∼2.3×10 8 M ○. , and they may be the remnants of an entity that was tidally disrupted by NGC 4254 and is now merging with it
A Complex Intrachromosomal Rearrangement Disrupting IRF6 in a Family with Popliteal Pterygium and Van der Woude Syndromes

Clefts of the lip and/or palate (CL/P) are considered the most common form of congenital anomalies occurring either in isolation or in association with other clinical features. Van der woude syndrome (VWS) is associated with about 2% of all CL/P cases and is further characterized by having lower lip pits. Popliteal pterygium syndrome (PPS) is a more severe form of VWS, normally characterized by orofacial clefts, lower lip pits, skin webbing, skeletal anomalies and syndactyly of toes and fingers. Both syndromes are inherited in an autosomal dominant manner, usually caused by heterozygous mutations in the Interferon Regulatory Factor 6 (IRF6) gene. Here we report the case of a two-generation family where the index presented with popliteal pterygium syndrome while both the father and sister had clinical features of van der woude syndrome, but without any point mutations detected by re-sequencing of known gene panels or microarray testing. Using whole genome sequencing (WGS) followed by local de novo assembly, we discover and validate a copy-neutral, 429 kb complex intra-chromosomal rearrangement in the long arm of chromosome 1, disrupting the IRF6 gene. This variant is copy-neutral, novel against publicly available databases, and segregates in the family in an autosomal dominant pattern. This finding suggests that missing heritability in rare diseases may be due to complex genomic rearrangements that can be resolved by WGS and de novo assembly, helping deliver answers to patients where no genetic etiology was identified by other means.
A reciprocity theorem for charge collection

It is shown that the current collected by a p‐n junction in presence of a unit point generation of carriers at a point P is the same (apart from the dimensions) as the excess minority‐carrier density at P due to a unit density of carriers at the junction edge. Use of this reciprocity relation may simplify the calculation of beam induced currents in semiconductor devices. The practical meaning of this property is illustrated in the case of a light‐emitting diode containing defects.
Refractive index of shock-compressed liquid nitrogen up to 29 GPa

ABSTRACT We report the equation of state and optical properties of shock-compressed liquid nitrogen (LN2) by using a two-stage light-gas gun at pressure up to 29 GPa. Laser velocimetry measurements were used to investigate the transparency and refractive index of shocked LN2 as a function of density. As the density increased with increasing pressure and temperature (13–25 GPa), the refractive index increased up to 27% of pre-shot index of LN2. Evidently, such extreme conditions had no major influence on molecules, and no such dissociation was observed up to 25 GPa. The polarizability slightly decreased and thus supported the existence of intact diatomic molecular nitrogen. At 29 GPa, shocked LN2 dissociated, showing that it probably changed to a highly reflecting fluid. Altogether, these experiments showed how the density affects the refractive index without any change in chemical bonding and allocates the condition at which the temperature-driven dissociation takes place.
Safety and Feasibility of Laparoscopic Parenchymal-Sparing Hepatectomy for Lesions with Proximity to Major Vessels in Posterosuperior Liver Segments 7 and 8

Simple Summary Improvements in perioperative management and surgical techniques have enabled laparoscopic liver resection for posterosuperior liver segments. Recent studies have reported the safety and feasibility of selected posterosuperior lesions; however, laparoscopic parenchymal-sparing hepatectomy for lesions with proximity to major vessels in posterosuperior segments has not yet been examined. The aim of this study is to examine the safety and feasibility of laparoscopic parenchymal-sparing hepatectomy for lesions with proximity to major vessels in posterosuperior segments 7 and 8. The present study demonstrated that laparoscopic parenchymal-sparing hepatectomy for lesions with proximity to major vessels in posterosuperior segments 7 and 8 is safe and feasible in a specialized center with a team experienced in laparoscopic liver surgery, and the HALS technique still plays an important role as minimally invasive liver resection. These findings suggest the possibility of taking steps to perform more advanced minimally invasive liver resections. Abstract Laparoscopic parenchymal-sparing hepatectomy (PSH) for lesions with proximity to major vessels (PMV) in posterosuperior segments (PSS) has not yet been sufficiently examined. The aim of this study is to examine the safety and feasibility of laparoscopic PSH for lesions with PMV in PSS 7 and 8. We retrospectively reviewed the outcomes of laparoscopic liver resection (LLR) and open liver resection (OLR) for PSS lesions and focused on patients who underwent laparoscopic PSH for lesions with PMV in PSS. Blood loss was lower in the LLR group (n = 110) than the OLR group (n = 16) (p = 0.009), and no other short-term outcomes were significantly different. Compared to the pure LLR group (n = 93), there were no positive surgical margins or complications in hand-assisted laparoscopic surgery (HALS) (n = 17), despite more tumors with PMV (p = 0.009). Regarding pure LLR for one tumor lesion, any short-term outcomes in addition to the operative time were not significantly different between the PMV (n = 23) and no-PMV (n = 48) groups. The present findings indicate that laparoscopic PSH for lesions with PMV in PSS is safe and feasible in a matured team, and the HALS technique still plays an important role.
Reduction of Plasma BCAAs following Roux-en-Y Gastric Bypass Surgery Is Primarily Mediated by FGF21

Type 2 diabetes (T2D) is a challenging health concern worldwide. A lifestyle intervention to treat T2D is difficult to adhere, and the effectiveness of approved medications such as metformin, thiazolidinediones (TZDs), and sulfonylureas are suboptimal. On the other hand, bariatric procedures such as Roux-en-Y gastric bypass (RYGB) are being recognized for their remarkable ability to achieve diabetes remission, although the underlying mechanism is not clear. Recent evidence points to branched-chain amino acids (BCAAs) as a potential contributor to glucose impairment and insulin resistance. RYGB has been shown to effectively lower plasma BCAAs in insulin-resistant or T2D patients that may help improve glycemic control, but the underlying mechanism for BCAA reduction is not understood. Hence, we attempted to explore the mechanism by which RYGB reduces BCAAs. To this end, we randomized diet-induced obese (DIO) mice into three groups that underwent either sham or RYGB surgery or food restriction to match the weight of RYGB mice. We also included regular chow-diet-fed healthy mice as an additional control group. Here, we show that compared to sham surgery, RYGB in DIO mice markedly lowered serum BCAAs most likely by rescuing BCAA breakdown in both liver and white adipose tissues. Importantly, the restored BCAA metabolism following RYGB was independent of caloric intake. Fasting insulin and HOMA-IR were decreased as expected, and serum valine was strongly associated with insulin resistance. While gut hormones such as glucagon-like peptide-1 (GLP-1) and peptide YY (PYY) are postulated to mediate various surgery-induced metabolic benefits, mice lacking these hormonal signals (GLP-1R/Y2R double KO) were still able to effectively lower plasma BCAAs and improve glucose tolerance, similar to mice with intact GLP-1 and PYY signaling. On the other hand, mice deficient in fibroblast growth factor 21 (FGF21), another candidate hormone implicated in enhanced glucoregulatory action following RYGB, failed to decrease plasma BCAAs and normalize hepatic BCAA degradation following surgery. This is the first study using an animal model to successfully recapitulate the RYGB-led reduction of circulating BCAAs observed in humans. Our findings unmasked a critical role of FGF21 in mediating the rescue of BCAA metabolism following surgery. It would be interesting to explore the possibility of whether RYGB-induced improvement in glucose homeostasis is partly through decreased BCAAs.
Critical Dynamics of Polymerized Membranes at the Crumpling Transition

Relaxation toward equilibrium of non-self-avoiding polymerized membrane is studied in the vicinity of the crumpling transition. The dynamics is shown to be that of a conserved order parameter with dynamical exponent z = 4 - η. Hidden supersymmetry is used to perform the calculation of z up to two-loop order.
Imaging a linearly or circularly polarized scene: micro-components and shrimp

Polarimetric imaging captures the polarization state of light from all the points of a scene. Snapshot polarimetric imaging collects the Stokes' parameters spatial distribution simultaneously. We will discuss state-of-the-art achievements and some fundamental diffraction limitations in polarimetric imaging with an array of micro-components. We will also look at the natural vision system of the mantis shrimp, with many of these same sensing abilities. The evolved and exquisite vision system possesses a recently-discovered circular polarization capability. This comprehensive polarization vision may enable imaging/communicating advantages in the underwater environment as well as more general turbid environments such as smoke and fog.
Integrating Fly Ash-Controlled Surface Morphology and Candle Grease Coating: Access to Highly Hydrophobic Poly (L-lactic Acid) Composite for Anti-Icing Application

New ways of recycling fly ash are of great significance for reducing the environmental pollution. In this work, biodegradable hydrophobic poly (L-lactic acid)/fly ash composites for anti-icing application were successfully fabricated via a facile solvent-volatilization-induced phase separation approach. A silane coupling agent of 3-(Trimethoxysilyl) propyl methacrylate was used to decorate a fly ash surface (FA@KH570) for strengthening the interface bonding between fly ash and poly (L-lactic acid). Moreover, FA@KH570 could obviously enhance the crystallinity of poly (L-lactic acid) (PLLA)/FA@KH570 composites, which accelerated the conversion from the liquid-liquid to the liquid-solid phase separation principle. Correspondingly, the controllable surface morphology from smooth to petal-like microspheres was attained simply by adjusting the FA@KH570 content. After coating nontoxic candle grease, the apparent contact angle of 5 wt% PLLA/FA@KH570 composite was significantly increased to an astonishing 151.2°, which endowed the composite with excellent anti-icing property. This strategy paves the way for recycling waste fly ash and manufacturing hydrophobic poly (L-lactic acid) composite for potential application as an anti-icing material for refrigerator interior walls.
Coumarin-Based Fluorescence Probe for Differentiated Detection of Biothiols and Its Bioimaging in Cells

In this work, a coumarin derivative, SWJT-14, was synthesized as a fluorescence probe to distinguish cysteine (Cys), homocysteine (Hcy) and glutathione (GSH) in aqueous solutions. The detection limit of Cys, Hcy and GSH for the probe was 0.02 μM, 0.42 μM and 0.92 μM, respectively, which was lower than biothiols in cells. The probe reacted with biothiols to generate different products with different conjugated structures. Additionally, it could distinguish Cys, Hcy and GSH using fluorescence and UV-Vis spectra. The detection mechanism was confirmed by MS. SWJT-14 was successfully used in cellular experiments and detected both endogenous and exogenous biothiols.
Lepton Flavour Violation in the Supersymmetric seesaw type-I

Oscillation experiments demand an avoidable extension to the Standard Model (SM) of particle physics. One of the simplest extensions is to introduce 3 heavy right-handed Majorana neutrinos (seesaw type-I). On the theoretical side, the hierarchy problem constitutes a solid hint for some more fundamental theory emerging at an energy scale . 3 Tev. For this, one of the most well motivated solutions is provided by Supersymmetry. In this thesis we follow these two a priori separate extensions to the SM. Since the smallness of neutrino masses is further justified by extremely heavy RH neutrinos, these will decouple from the low energy theory. Unsatisfactorily, all that could be known about their existence is just what we already know: neutrino masses. This general statement is no longer valid when seesaw is embedded in some more fundamental model with which it can communicate. This is exactly what happens in the supersymmetric seesaw. In this thesis we will study the lepton flavour violation (LFV) processes that originate from the presence of these right-handed neutrinos in the context of the minimal supersymmetric standard model (MSSM) with mSUGRA (minimal supergravity) boundary conditions. There are already interesting bounds [1] on LFV rates, especially in the radiative decay μ → e γ, specifically, BR(μ → e γ) ≤ 1.2 × 10−11, constraining simultaneously the MSSM parameter space and the seesaw parameters.