Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Yangtze River on population genetic structure of the relict plant Parrotia subaequalis in eastern China

Abstract Parrotia subaequalis (Hamamelidaceae) is a Tertiary relic species endemic in eastern China. We used inter‐simple sequence repeat (ISSR) markers to access genetic diversity and population genetic structure in natural five populations of P. subaequalis. The levels of genetic diversity were higher at species level (H = 0.2031) but lower at population level (H = 0.1096). The higher genetic diversity at species levels might be attributed to the accumulation of distinctive genotypes which adapted to the different habitats after Quaternary glaciations. Meanwhile, founder effects on the early stage, and subsequent bottleneck of population regeneration due to its biological characteristics, environmental features, and human activities, seemed to explain the low population levels of genetic diversity. The hierarchical AMOVA revealed high levels (42.60%) of among‐population genetic differentiation, which was in congruence with the high levels of Nei's genetic differentiation index (GST = 0.4629) and limited gene flow (N m = 0.5801) among the studied populations. Mantel test showed a significant isolation‐by‐distance, indicating that geographic isolation has a significant effect on genetic structure in this species. Unweighted pair‐group method with arithmetic average clustering, PCoA, and Bayesian analyses uniformly recovered groups that matched the geographical distribution of this species. In particular, our results suggest that Yangtze River has served as a natural barrier to gene flow between populations occurred on both riversides. Concerning the management of P. subaequalis, the high genetic differentiation among populations indicates that preserving all five natural populations in situ and collecting enough individuals from these populations for ex situ conservation are necessary.
Machine learning for chronic disease

Chronic disease is a hugely growing healthcare burden, with patients experiencing symptoms and requiring therapy throughout life. Studies in the USA have found that, with direct healthcare costs combined with lost productivity, the total economic cost of diabetes, heart disease, and hypertension was over 300 billion dollars annually from 2008 to 2010 [1]. Within this chapter, much of our motivation will be from the application area of inflammatory bowel disease (IBD), a chronic disease characterised by severe gastrointestinal inflammation. Approximately 620,000 patients in the UK have IBD, with estimates of healthcare costs per patient ranging from £631 to £3,000 per year [2]. IBD incidence is growing throughout the world, making efforts to better understand the underlying disease pathophysiology all the more important [3]. Within chronic disease, there are a variety of clinical areas in which machinelearning approaches can provide clinical value. Here, we will start with an overview of the types of data that may be encountered in the setting of chronic disease. We will then explain how extreme value theory (EVT) can be applied to better quantify severity and risk in chronic disease, and we will finally introduce a variety of methods for examining underlying patient subgroups within heterogeneous diseases.
Socioeconomic status and quality of life among Chinese American breast cancer survivors: The mediating roles of social support and social constraints

Literature has well noted ethnic/racial disparities in cancer survival and cancer care. However, socioeconomic disparities in psychosocial adjustment to breast cancer have garnered little attention. This study addresses the research gap by investigating the associations between socioeconomic indicators (ie, education, annual personal, and household income) and quality of life (QOL) and the mediating roles of social support and social constraints (objective and subjective conditions that constrain individuals from disclosing cancer concerns) in these associations among Chinese American breast cancer survivors (CABCS).
JAM 3 maintains leukemia-initiating cell self-renewal through LRP 5 / AKT / b-catenin / CCND 1 signaling

Leukemia-initiating cells (LICs) are responsible for the initiation, development, and relapse of leukemia. The identification of novel therapeutic LIC targets is critical to curing leukemia. In this report, we reveal that junctional adhesion molecule 3 (JAM3) is highly enriched in both mouse and human LICs. Leukemogenesis is almost completely abrogated upon Jam3 deletion during serial transplantations in an MLL-AF9–induced murine acute myeloid leukemia model. In contrast, Jam3 deletion does not affect the functions of mouse hematopoietic stem cells. Moreover, knockdown of JAM3 leads to a dramatic decrease in the proliferation of both human leukemia cell lines and primary LICs. JAM3 directly associates with LRP5 to activate the downstream PDK1/AKT pathway, followed by the downregulation of GSK3b and activation of b-catenin/CCND1 signaling, to maintain the self-renewal ability and cell cycle entry of LICs. Thus, JAM3 may serve as a functional LIC marker and play an important role in the maintenance of LIC stemness through unexpected LRP5/PDK1/AKT/GSK3b/b-catenin/CCND1 signaling pathways but not via its canonical role in cell junctions and migration. JAM3 may be an ideal therapeutic target for the eradication of LICs without influencing normal hematopoiesis. Research Article Hematology Stem cells
Molecule‐Doped Nickel Oxide: Verified Charge Transfer and Planar Inverted Mixed Cation Perovskite Solar Cell

Both conductivity and mobility are essential to charge transfer by carrier transport layers (CTLs) in perovskite solar cells (PSCs). The defects derived from generally used ionic doping method lead to the degradation of carrier mobility and parasite recombinations. In this work, a novel molecular doping of NiOx hole transport layer (HTL) is realized successfully by 2,2′‐(perfluoronaphthalene‐2,6‐diylidene)dimalononitrile (F6TCNNQ). Determined by X‐ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy, the Fermi level (EF) of NiOx HTLs is increased from −4.63 to −5.07 eV and valence band maximum (VBM)‐EF declines from 0.58 to 0.29 eV after F6TCNNQ doping. The energy level offset between the VBMs of NiOx and perovskites declines from 0.18 to 0.04 eV. Combining with first‐principle calculations, electrostatic force microscopy is applied for the first time to verify direct electron transfer from NiOx to F6TCNNQ. The average power conversion efficiency of CsFAMA mixed cation PSCs is boosted by ≈8% depending on F6TCNNQ‐doped NiOx HTLs. Strikingly, the champion cell conversion efficiency of CsFAMA mixed cations and MAPbI3‐based devices gets to 20.86% and 19.75%, respectively. Different from passivation effect, the results offer an extremely promising molecular doping method for inorganic CTLs in PSCs. This methodology definitely paves a novel way to modulate the doping in hybrid electronics more than perovskite and organic solar cells.
4 Intelligent Electronic Health Systems

Healthcare systems worldwide are entering a new phase: ever-increasing quantities of complex, massively multivariate data concerning all aspects of patient care are starting to be routinely acquired and stored [1], throughout the life of a patient. This exponential growth in data quantities far outpaces the capability of clinical experts to cope, resulting in a so-called data deluge, in which the data are largely unexploited. There is huge potential for using advances in large-scale machine learning methodologies* to exploit the contents of these complex data sets by performing robust, scalable, automated inference to improve healthcare outcomes significantly by using patient-specific probabilistic models, a field in which there is little existing research [2] and which promises to develop into a new
The Association Between Transportation and Life-Space Mobility in Community-Dwelling Older People With or Without Walking Difficulties

Objective: The aim of this study is to examine whether a persons’ most frequently used mode of transportation is associated with life-space mobility and whether the association differs between persons with or without walking difficulties. Method: Life-space mobility was measured with the Life-Space Assessment in 848 community-dwelling men and women aged 75 to 90 years. Six separate mobility groups were formed according to the most frequently used mode of transportation (car driver, car passenger, public transportation) combined with the presence or absence of difficulties walking 2 km. Results: Car drivers without walking difficulties had the highest life-space mobility scores, and car passengers with walking difficulties had the lowest scores. Mode of transportation influenced the odds for restricted life space differently depending on whether or not the person had walking difficulties. Discussion: To support community mobility among older persons, it would be important to improve different transportation options to meet older persons’ individual wishes, needs, and resources.
Effect of supplementation with cobalamin carried either by a milk product or a capsule in mildly cobalamin-deficient elderly Dutch persons.

BACKGROUND A high prevalence of cobalamin deficiency occurs in the elderly population, which may be treated orally or with injections. Little is known about the relative bioavailability of crystalline cobalamin added to food products. OBJECTIVE The objective was to assess the effect of supplementation with 1000 microg crystalline cobalamin, carried either by a milk product or a capsule, on cobalamin status in mildly cobalamin-deficient elderly Dutch persons. DESIGN Two double-blind randomized controlled intervention studies, each covering a 12-wk supplementation period, were carried out in parallel. Mildly cobalamin-deficient elderly persons (n = 112) were separately recruited for the milk and capsule trials. Mild cobalamin deficiency was defined as a cobalamin concentration between 100 and 300 pmol/L and a plasma methylmalonic acid (MMA) concentration > or = 0.30 micromol/L. Allocation to the placebo or cobalamin carrier was carried out independently in both trials. RESULTS In the fortified-milk group, the mean (+/-SD) increase in serum cobalamin was 250 +/- 96 pmol/L, the median (5th and 95th percentiles) decrease in plasma MMA was 0.19 (-0.76, -0.04) micromol/L, and the median decrease in plasma homocysteine was 4.0 (-7.3, 3.0) micromol/L. All changes were significantly different from those in the placebo milk group (P < 0.01). Likewise, in the cobalamin-capsule group, the mean increase in serum cobalamin was 281 +/- 136 pmol/L, the median decrease in plasma MMA was 0.18 (-2.95, 0.14) micromol/L, and the median decrease in plasma homocysteine was 1.8 (-10.6, 2.4) micromol/L; all changes were significantly different from those in the placebo capsule group (P < 0.01). No significant differences were observed between the fortified-milk and capsule groups (P > 0.40). CONCLUSION Crystalline cobalamin added to milk is an effective alternative to cobalamin capsules for improving cobalamin status.
Greater Cervical Muscle Fat Infiltration Evaluated by Magnetic Resonance Imaging is Associated With Poor Postural Stability in Patients With Cervical Spondylotic Radiculopathy

Study Design. A population-based, cross-sectional study. Objective. The aim of this study was to quantitatively evaluate the relationship between static postural stability and fat infiltration within cervical multifidus muscle in patients with cervical spondylotic radiculopathy (CSR). Summary of Background Data. CSR causes denervation by compression of nerve roots. This denervation is detected by fatty infiltration or results in fatty infiltration within muscles. Proprioceptive information in cervical multifidus muscle plays an important role in coordinated movement of postural stability; however, there have been few studies evaluating the relationship between postural stability and fat infiltration within cervical multifidus muscle among CSR patients. Methods. Sixteen CSR patients with C6 injuries and 25 age-matched healthy controls underwent magnetic resonance images to examine bilateral cervical multifidus muscle. For evaluation of fat within muscle, a muscle fat index (MFI) was calculated by using both measurement of cervical multifidus muscle and intermuscular fat. Participants’ postural stability at upright position with eyes-opened and eyes-closed for 60 seconds was examined by a platform. Two parameters, the total length and the area of the center of pressure (COP), were used for evaluation. Results. The CSR group showed significantly poorer postural stability than the control group (eyes-opened the total length; P < 0.05, eyes-closed the total length; P < 0.05, eyes-closed the area; P < 0.05). There were significant group differences at C4, C5, and C6 MFI (P < 0.05). In the CSR group, a correlation analysis demonstrated that the age, C4, C5, and C6 MFI values were significantly associated with the eyes-closed the total length of the COP (P < 0.05). Conclusions. Fat infiltration within muscle could lead to inhibition of normal activity of musculature. The present study suggests that fat within cervical multifidus muscle could directly cause postural instability in static standing, even though the proprioceptive information has normal lower limbs. Level of Evidence: 3
An Efficient FPGA Based HDB3 Decoding System Using Direct Digital Synthesis

The proposed design of HDB3 decoding system using FPGA implementation offers an efficient and unfailing decoding at receiving end by sustaining clock data recovery using Direct Digital Synthesis (DDS). The system captures E1/T1 HDB3 encoded tertiary level stream at input, converts it into binary level symbols, FPGA IO reconcilable, and decode and transforms it into synchronized NRZ output. The receiver end of FPGA based HDB3 decoding system has never been implemented using clock data recovery. The resource efficient implementation and synthesis outcome illustrate that the design of HDB3 decoder is very simple and fault tolerant and its ASIC design can easily be surrogate by the proposed idea.
Decreased water limitation under elevated CO2 amplifies potential for forest carbon sinks

Significance With increasing atmospheric CO2 and a changing climate come changes in both plant water use efficiency and rainfall regimes. The effects of these changes on forests, including feedbacks to the carbon cycle, are complex. Through a theoretical analysis combining CO2, soil moisture dynamics, and individual-based competition in forests, we find that (i) carbon storage has a complex and significant dependence on rainfall amount and timing and (ii) the main effect of increasing CO2 in water-limited forests is a decrease in the amount of time trees spend in water limitation. This main effect is predicted to reduce competitive overinvestment in fine roots, drive competitive trees to increase investment in woody biomass, and greatly increase forest carbon storage in live biomass. Increasing atmospheric CO2 concentrations and changing rainfall regimes are creating novel environments for plant communities around the world. The resulting changes in plant productivity and allocation among tissues will have significant impacts on forest carbon storage and the global carbon cycle, yet these effects may depend on mechanisms not included in global models. Here we focus on the role of individual-level competition for water and light in forest carbon allocation and storage across rainfall regimes. We find that the complexity of plant responses to rainfall regimes in experiments can be explained by individual-based competition for water and light within a continuously varying soil moisture environment. Further, we find that elevated CO2 leads to large amplifications of carbon storage when it alleviates competition for water by incentivizing competitive plants to divert carbon from short-lived fine roots to long-lived woody biomass. Overall, we find that plant dependence on rainfall regimes and plant responses to added CO2 are complex, but understandable. The insights developed here will serve as an important foundation as we work to predict the responses of plants to the full, multidimensional reality of climate change, which involves not only changes in rainfall and CO2 but also changes in temperature, nutrient availability, and disturbance rates, among others.
Image Spatial Verification using Segment Intersection of Interest Points

This work presents a new spatial verification technique for image similarity search. The proposed algorithm evaluates the geometry of the detected local keypoints by building segments connecting pairs of points and analyzing their intersections in a 2D plane. We show that these intersections remain constant with respect to different geometric transformations (translation, rotation, similarity and affine). Evaluation has been performed obtaining an initial image similarity ranking with a BOF-based methodology, and then using the proposed method for reranking. The presented algorithm (SIIP) has been compared to the RANSAC spatial verification method, showing that it is more efficient and obtains a higher performance on three different datasets.
Evolution of robustness in the signaling network of Pristionchus vulva development

Robustness to environmental or genetic perturbation, like any other trait, is affected by evolutionary change. However, direct studies on the interplay of robustness and evolvability are limited and require experimental microevolutionary studies of developmental processes. One system in which such microevolutionary studies can be performed is vulva development in the nematode Pristionchus pacificus. Three vulval precursor cells respond to redundant cell–cell interactions, including signals from the gonad and the epidermal cell P8.p. Interestingly, P. pacificus P8.p is involved in cell fate specification of the future vulva cells by lateral inhibition but is incompetent to respond to the inductive signal from the gonad itself. These functional properties of P8.p are unknown from other nematodes, such as Caenorhabditis elegans. We began an experimental and genetic analysis of the microevolution of P8.p function. We show that vulva misspecification events differ between Pristionchus strains and species. Similarly, lateral inhibition and developmental competence of P8.p evolved within the genus Pristionchus and between natural isolates of P. pacificus. Surprisingly, in some recombinant inbred lines of two distinct P. pacificus isolates, P8.p gained competence to form vulva tissue, a trait that was never observed in P. pacificus isolates. Our results suggest differences in developmental stability between natural isolates, and we hypothesize that the remarkable evolvability of redundant cell–cell interactions allows for adaptive evolution of robustness to developmental noise.
Post‐transplant bendamustine reduces GvHD while preserving GvL in experimental haploidentical bone marrow transplantation

Advances in haploidentical bone marrow transplantation (h‐BMT) have drastically broadened the treatment options for patients requiring BMT. The possibility of significantly reducing the complications resulting from graft‐versus‐host disease (GvHD) with the administration of post‐transplant cyclophosphamide (PT‐CY) has substantially improved the efficacy and applicability of T cell‐replete h‐BMT. However, higher frequency of disease recurrence remains a major challenge in h‐BMT with PT‐CY. There is a critical need to identify novel strategies to prevent GvHD while sparing the graft‐versus‐leukaemia (GvL) effect in h‐BMT. To this end, we evaluated the impact of bendamustine (BEN), given post‐transplant, on GvHD and GvL using clinically relevant murine h‐BMT models. We provide results indicating that post‐transplant bendamustine (PT‐BEN) alleviates GvHD, significantly improving survival, while preserving engraftment and GvL effects. We further document that PT‐BEN can mitigate GvHD even in the absence of Treg. Our results also indicate that PT‐BEN is less myelosuppressive than PT‐CY, significantly increasing the number and proportion of CD11b+Gr‐1hi cells, while decreasing lymphoid cells. In vitro we observed that BEN enhances the suppressive function of myeloid‐derived suppressor cells (MDSCs) while impairing the proliferation of T‐ and B‐cells. These results advocate for the consideration of PT‐BEN as a new therapeutic platform for clinical implementation in h‐BMT.
4 Degrees of Expertise

Visual object recognition and categorization are fundamental abilities required for successful negotiation of the visual world. Humans effortlessly classify and recognize objects and faces within busy scenes, thousands of times a day. Thus, understanding how perceptual categorization and learning occur and how such seemingly complicated computations are implemented in brain processes is an important goal in cognitive psychology and cognitive neuroscience. One way of furthering our understanding of category learning is to examine how differences in experience with specific classes of objects (e.g., dogs, cars, faces) influence the speed and level at which these objects are categorized. Object categorization is arbitrary in the sense that a single object can be classified at multiple levels of abstraction. For instance, the same American Tree Sparrow can be classified as an ‘‘animal’’ at a general or superordinate level, a ‘‘bird’’ at the basic level, and an ‘‘American Tree Sparrow’’ at a specific or subordinate level. In contrast to object categorization, object recognition is not arbitrary in that most objects are identified at the same level of abstraction—the so-called basic level (Jolicoeur, Gluck, & Kosslyn, 1984; Murphy & Smith, 1982; Rosch, Mervis, Gray, Johnson, & Boyes-Braem, 1976). Seminal work by Rosch and colleagues demonstrated that the basic level is the optimum level of abstraction at which category members are perceptually most similar to one another and are maximally distinct from other category members. Given its structural advantage, the basic level is the preferred level in initial object recognition. However, the basic level is typically not the preferred level for experts where recognition often demands a more specific, subordinate level of identification (Johnson & Mervis, 1997; Tanaka, 2001; but see Wong & Gauthier, in press, and Chapter 10, for descriptions of basic-level expertise). For example, face processing is thought to be a universally expert skill where faces are differentiated at the level of the individual (e.g., Bob, Susan) (Tanaka, 2001). Similarly, given the demands of expertise, expert bird watchers and car enthusiasts identify birds or cars at a more subordinate level (e.g., Bachman warbler, BMW Z1) compared to nonexperts (Tanaka & Taylor, 1991). Tanaka & Taylor (1991) suggested that category specificity arises when the demands of expertise require that exemplars within a category be differentiated from one another (as we do with faces). Furthermore, different recognition strategies may be best supported by different parts of