Miracle-dz/UniFAR-FTUs huggingface dataset:
Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates

Tarsiers are small nocturnal primates with a long history of fuelling debate on the origin and evolution of anthropoid primates. Recently, the discovery of M and L opsin genes in two sister species, Tarsius bancanus (Bornean tarsier) and Tarsius syrichta (Philippine tarsier), respectively, was interpreted as evidence of an ancestral long-to-middle (L/M) opsin polymorphism, which, in turn, suggested a diurnal or cathemeral (arrhythmic) activity pattern. This view is compatible with the hypothesis that stem tarsiers were diurnal; however, a reversion to nocturnality during the Middle Eocene, as evidenced by hyper-enlarged orbits, predates the divergence of T. bancanus and T. syrichta in the Late Miocene. Taken together, these findings suggest that some nocturnal tarsiers possessed high-acuity trichromatic vision, a concept that challenges prevailing views on the adaptive origins of the anthropoid visual system. It is, therefore, important to explore the plausibility and antiquity of trichromatic vision in the genus Tarsius. Here, we show that Sulawesi tarsiers (Tarsius tarsier), a phylogenetic out-group of Philippine and Bornean tarsiers, have an L opsin gene that is more similar to the L opsin gene of T. syrichta than to the M opsin gene of T. bancanus in non-synonymous nucleotide sequence. This result suggests that an L/M opsin polymorphism is the ancestral character state of crown tarsiers and raises the possibility that many hallmarks of the anthropoid visual system evolved under dim (mesopic) light conditions. This interpretation challenges the persistent nocturnal–diurnal dichotomy that has long informed debate on the origin of anthropoid primates.
Adjuvant Chemotherapy Use and Health Care Costs After Introduction of Genomic Testing in Breast Cancer.

PURPOSE We assessed the associations between the 21-gene recurrence score assay (RS) receipt, subsequent chemotherapy use, and medical expenditures among patients with early-stage breast cancer. PATIENTS AND METHODS Data from the Pennsylvania Cancer Registry were used to assemble a retrospective cohort of women with early-stage breast cancer from 2007 to 2010 who underwent initial surgical treatment. These data were merged with administrative claims from the 12-month periods before and after diagnosis to identify comorbidities, treatments, and expenditures (n = 7,287). Propensity score-weighted regression models were estimated to identify the effects of RS receipt on chemotherapy use and medical spending in the year after diagnosis. RESULTS The associations between RS receipt and outcomes varied markedly by patient age. RS use was associated with lower chemotherapy use among women younger than 55 (19.2% lower; 95% CI, 10.6 to 27.9). RS use was associated with higher chemotherapy use among women 75 to 84 years old (5.7% higher; 95% CI, 0.4 to 11.0). RS receipt was associated with lower adjusted 1-year medical spending among women younger than 55 ($15,333 lower; 95% CI, $2,841 to $27,824) and with higher spending among women who were 75 to 84 years old ($3,489 higher; 95% CI, $857 to $6,122). CONCLUSION RS receipt was associated with reduced use of adjuvant chemotherapy and lower health care spending among women with breast cancer who were younger than 55. Conversely, among women 75 and older, RS testing was associated with a modest increase in chemotherapy use and slightly higher spending. From a population perspective, the impact of RS testing on breast cancer treatment and health care costs is much greater in younger women.
On strictly weak mixing C*-dynamical systems and a weighted ergodic theorem

We prove that unique ergodicity of tensor product of a C *-dynamical system implies its strictly weak mixing. By means of this result a uniform weighted ergodic theorem with respect to S -Besicovitch sequences for strictly weak mixing dynamical systems is proved. Moreover, we provide certain examples of strictly weak mixing dynamical systems.
Differential Requirements of TCR Signaling in Homeostatic Maintenance and Function of Dendritic Epidermal T Cells

Dendritic epidermal T cells (DETCs) are generated exclusively in the fetal thymus and maintained in the skin epithelium throughout postnatal life of the mouse. DETCs have restricted antigenic specificity as a result of their exclusive usage of a canonical TCR. Although the importance of the TCR in DETC development has been well established, the exact role of TCR signaling in DETC homeostasis and function remains incompletely defined. In this study, we investigated TCR signaling in fully matured DETCs by lineage-restricted deletion of the Lat gene, an essential signaling molecule downstream of the TCR. We found that Lat deletion impaired TCR-dependent cytokine gene activation and the ability of DETCs to undergo proliferative expansion. However, linker for activation of T cells–deficient DETCs were able to maintain long-term population homeostasis, although with a reduced proliferation rate. Mice with Lat deletion in DETCs exhibited delayed wound healing accompanied by impaired clonal expansion within the wound area. Our study revealed differential requirements for TCR signaling in homeostatic maintenance of DETCs and in their effector function during wound healing.
SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins

Indels in the coding regions of a gene can either cause frameshifts or amino acid insertions/deletions. Frameshifting indels are indels that have a length that is not divisible by 3 and subsequently cause frameshifts. Indels that have a length divisible by 3 cause amino acid insertions/deletions or block substitutions; we call these 3n indels. The new amino acid changes resulting from 3n indels could potentially affect protein function. Therefore, we construct a SIFT Indel prediction algorithm for 3n indels which achieves 82% accuracy, 81% sensitivity, 82% specificity, 82% precision, 0.63 MCC, and 0.87 AUC by 10-fold cross-validation. We have previously published a prediction algorithm for frameshifting indels. The rules for the prediction of 3n indels are different from the rules for the prediction of frameshifting indels and reflect the biological differences of these two different types of variations. SIFT Indel was applied to human 3n indels from the 1000 Genomes Project and the Exome Sequencing Project. We found that common variants are less likely to be deleterious than rare variants. The SIFT indel prediction algorithm for 3n indels is available at http://sift-dna.org/
Office hysteroscopy.

Diagnostic, panoramic hysteroscopy can be performed in an office setting with small discomfort to the patient. The procedure enables the physician to search for organic intrauterine abnormalities and to select the proper form of therapy based on the observations. Often no pathology is seen and further surgical interventions are not needed. This operation currently represents the state of the art for investigation of the endometrial cavity. In the future it will become the standard of care as the first step for evaluation of causes of abnormal uterine bleeding in selected patients.
Fast and Reliable Browser Identiﬁcation with JavaScript Engine Fingerprinting

—Web browsers are crucial software components in today’s usage of the Internet, but the reliable detection of whether a client is using a speciﬁc browser can still be considered a nontrivial problem. Reliable browser identiﬁcation is crucial for online security and privacy e.g., regarding drive-by downloads and user tracking, and can be used to enhance the user’s security. So far the UserAgent string is often used to identify a given browser, but it is a self-reported string provided by the client and can be changed arbitrarily. In this paper we propose a new method for identifying web browsers based on the underlying Javascript engine, which can be executed on the client side within a fraction of a second. Our method is three orders of magnitude faster than previous work on Javascript engine ﬁngerprinting, and can be implemented with well below a few hundred lines of code. We show the feasibility of our method with a survey and discuss the consequences for user privacy and browser security. Furthermore, we collected data for more than 150 browser and operating system combinations, and present algorithms to make browser identiﬁcation as fast as possible. UserAgent string modiﬁcations become easily detectable with JavaScript engine ﬁngerprinting, which is shown exemplarily on the Tor browser bundle as it uses a uniform UserAgent string across different browser versions. Finally, we propose to use our results for enhancing state-of-the-art session management (with or without SSL), as reliable browser identiﬁcation can be used to increase the complexity of session hijacking attacks considerably.
Transient Global Amnesia and Migraine

A 31-year-old woman presented with a history of transient memory problems. The day before, upon awakening at her normal time, she had trouble with her memory such as remembering events of the day before, the day of a dinner engagement the week before, and a movie she saw a week ago. The memory problem lasted all day and resolved by the next morning. Her father stated that her speech was normal but she just seemed confused. She had no associated headache or other neurologic or systemic symptoms or signs. There is a history of migraine without aura from childhood until 10 years ago and migraine aura without headache occurring once every couple of months for the past several years. Past medical history was otherwise negative. Neurological examination was normal. A MRI scan of the brain, complete blood count, chemistry profile, TSH, and vitamin B12 level were all normal. Question. —Is there a relationship between transient global amnesia and migraine?
Parsing neural mechanisms of social and physical risk identifications

Psychometric studies of risk perception have categorized personal risks into social and physical domains. To investigate whether and how the human brain differentiates social and physical risks, we scanned human adults using functional magnetic resonance imaging when they identified potential risks involved in social and physical behaviors. We found that the identification of risky behaviors in both domains induced increased activations in the anterior medial prefrontal cortex (MPFC, BA9/10)/ventral anterior cingulate (ACC) and posterior cingulate (PCC) relative to identification of safe behaviors. However, social risks induced stronger anterior MPFC activation whereas physical risks were associated with stronger ventral ACC activity. In addition, anterior MPFC activity was negatively correlated with the rating scores of the degree of social risk whereas PCC activity was positively correlated with the rating scores of the degree of physical risk. Relative to an autobiographical control task, the social risk identification task induced stronger sustained activity in the left supplementary motor area/dorsal ACC and increased transient activity in bilateral posterior insula. The physical risk identification task, however, resulted in stronger sustained activity in the right cuneus/precuneus and increased transient activation in bilateral amygdala. Our results indicate the existence of distinct neural mechanisms underlying social and physical risk identifications and provide neural bases for the psychometric categorization of risks into different domains. Hum Brain Mapp, 2009. © 2008 Wiley‐Liss, Inc.
Patients’ Attitudes Toward Electronic Health Information Exchange: Qualitative Study

Background In many countries, there has been substantial progress in establishing the electronic transmission of patients’ health information between health care providers, but little is known about how best to engage patients in the process. Objective We explored patients’ views about sharing of electronic health information and their preferences for learning about and participating in this process. Methods Patients in one Massachusetts community in the northeastern United States were recruited to participate in focus-group discussions. Prior to discussion, participants completed a written questionnaire that captured their reactions to draft educational materials and a consent form. The discussion moderator and two physicians analyzed the moderator’s detailed notes from each session and participants’ written comments, using an immersion-crystallization approach. Results Three dominant themes emerged: (1) concerns about privacy and security, (2) the potential benefit to a person’s health, and (3) the desire for more information about the consent process. On the pre-discussion questionnaire, 55 out of 62 participants (88%) indicated that they would provide consent for their information to be shared electronically among their health care providers, given the materials they had reviewed. Conclusions Patients are enthusiastic about electronic health information exchange, recognizing its capacity to improve the quality and safety of health care; however, they are also concerned about its potential to result in breached privacy and misuse of health data. As the exchange of electronic health information becomes more widespread, policy makers will need to ensure that patients have access to concise educational materials and opportunities to engage in conversations about the risks and benefits of participation.
A New Convergence Proof of Fuzzy c-Means

In this letter, we give a new, more direct derivation of the convergence properties of the fuzzy c-means (FCM) algorithm, using the equivalence between the original and reduced FCM criterion. From the point of view of the reduced criterion, the FCM algorithm is simply a steepest descent algorithm with variable steplength. We prove that steplength adjustment follows from the majorization principle for steplength. By applying the majorization principle we give a straightforward proof of global convergence. Further convergence properties follow immediately using known results of optimization theory
Bidirectional Modulation of Substantia Nigra Activity by Motivational State

A major output nucleus of the basal ganglia is the substantia nigra pars reticulata, which sends GABAergic projections to brainstem and thalamic nuclei. The GABAergic (GABA) neurons are reciprocally connected with nearby dopaminergic neurons, which project mainly to the basal ganglia, a set of subcortical nuclei critical for goal-directed behaviors. Here we examined the impact of motivational states on the activity of GABA neurons in the substantia nigra pars reticulata and the neighboring dopaminergic (DA) neurons in the pars compacta. Both types of neurons show short-latency bursts to a cue predicting a food reward. As mice became sated by repeated consumption of food pellets, one class of neurons reduced cue-elicited firing, whereas another class of neurons progressively increased firing. Extinction or pre-feeding just before the test session dramatically reduced the phasic responses and their motivational modulation. These results suggest that signals related to the current motivational state bidirectionally modulate behavior and the magnitude of phasic response of both DA and GABA neurons in the substantia nigra.
Archaeological Evidence for Peach (Prunus persica) Cultivation and Domestication in China

The cultivated/domesticated peach (Prunus persica var. persica; Rosaceae, subgenus Amygdalus; synonym: Amygdalus persica) originated in China, but its wild ancestor, as well as where, when, and under what circumstances the peach was domesticated, is poorly known. Five populations of archaeological peach stones recovered from Zhejiang Province, China, document peach use and evolution beginning ca. 8000 BP. The majority of the archaeological sites from which the earliest peach stones have been recovered are from the Yangzi River valley, indicating that this is where early selection for favorable peach varieties likely took place. Furthermore, peach stone morphology through time is consistent with the hypothesis that an unknown wild P. persica was the ancestor of the cultivated peach. The oldest archaeological peach stones are from the Kuahuqiao (8000–7000 BP) and Tianluoshan (7000–6500 BP) sites and both stone samples segregate into two size groups, suggesting early selection of preferred types. The first peach stones in China most similar to modern cultivated forms are from the Liangzhu culture (ca. 5300 to 4300 BP), where the peach stones are significantly larger and more compressed than earlier stones. Similar peach stones are reported from Japan much earlier (6700–6400 BP). This large, compressed-stone peach was introduced to Japan and indicates a yet unidentified source population in China that was similar to the Liangzhu culture peach. This study proposes that the lower Yangzi River valley is a region, if not the region, of early peach selection and domestication and that the process began at least 7500 years ago.
Bone marrow biopsy in patients with hepatitis C virus infection: Spectrum of findings and diagnostic utility

Patients with hepatitis C virus (HCV) infection develop a number of hematologic disorders, with benign and malignant B‐cell proliferations being the most common. HCV‐infected patients are also prone to developing peripheral cytopenias, the etiologies of which are multifactorial and include hypersplenism and/or antiviral medications. Some of these patients may undergo bone marrow biopsy but no study has systematically recorded the bone marrow findings in this patient group. Here, we report on the range of bone marrow findings in 47 adult HCV‐infected patients. These patients, who lacked concurrent human immunodefiency virus (HIV) infection, most commonly presented for a bone marrow biopsy due to abnormal peripheral cell counts. The bone marrow biopsies displayed a range of findings. Dyserythropoiesis, present in 19% of the cases, was the most common finding. Patients with pancytopenia(n = 6), as defined by current World Health Organization standards, were the most likely to have bone marrow abnormalities; two pancytopenic patients had acute myeloid leukemia, and one patient had a primary myelodysplastic syndrome. There was no correlation in bone marrow findings and antiviral medications, MELD score, cirrhosis or splenomegaly, suggesting that the degree of bone marrow dysfunction is independent of stage of HCV. The results of this study suggest that bone marrow biopsy in HCV‐infected patients, even those with features of hypersplenism and/or documented antiviral therapy, can be a valid test for hematologic evaluation, especially for patients with severe pancytopenia and/or sudden alterations in peripheral cell counts. Am. J. Hematol. 85:106–110, 2010. © 2009 Wiley‐Liss, Inc.
Contribution of microglia/macrophages to expansion of infarction and response of oligodendrocytes after focal cerebral ischemia in rats.

BACKGROUND AND PURPOSE The purpose of this study was (1) to examine the contribution of microglia and macrophages with their interleukin-1beta production and (2) to assess the vulnerability and response of oligodendrocytes in cerebral infarction. METHODS Male Wistar rats were subjected to permanent occlusion of the left middle cerebral artery. Expansion of ischemic infarction and response of oligodendrocytes were investigated together with accumulation of inflammatory cells, production of interleukin-1beta, and disruption of the blood-brain barrier. Apoptotic cell death was inferred from fragmented DNA and the expression of proapoptotic Bax protein. RESULTS During expansion of infarction, amoeboid microglia and extravasation of serum albumin were observed not only in the infarcted area but also in the adjacent surviving area, whereas macrophages accumulated along the boundary and granulocytes migrated into the center of the infarction. Both amoeboid microglia and macrophages produced interleukin-1beta, an inflammatory cytokine, during an early ischemic period. Furthermore, macrophages within the infarcted tissue expressed Bax protein and subsequently showed fragmented nuclear DNA. Oligodendrocytes were detected in the infarcted area even after 24 hours following middle cerebral artery occlusion, but they subsequently developed fragmented DNA. A week after onset of ischemia, oligodendrocytes were found to be accumulated in the intact area bordered with the infarct together with reactive astrocytes. CONCLUSIONS Our results suggest the importance of amoeboid microglia, macrophages, and their interleukin-1beta production in gradual expansion of cerebral infarction. Resident oligodendrocytes may be resistant to ischemic insults, and oligodendrocytes accumulated at the border of the infarction may participate in tissue repair after cerebral infarction.
A replicated study on correlating agile team velocity measured in function and story points

Since the rapid growth of agile development methods for software engineering, more and more organizations measure the size of iterations, releases, and projects in both function points and story points. In 2011 Santana et al. performed a case study on the relation between function points and story points, from data collected in a Brazilian Government Agency. In this paper we replicate this study, using data collected in a Dutch banking organization. Based on a statistical correlation test we find that a comparison between function points and story points as measured in our repository indicates a moderate negative linear relation, where Santana et al. concluded a strong positive linear relation between both size metrics in their case study. Based on the outcome of our study we conclude that it appears too early to make generic claims on the relation between function points and story points; in fact FSM-theory seems to underpin that such a relationship is a spurious one.
Poststroke dementia is associated with recurrent ischaemic stroke

Objective To investigate whether poststroke dementia (PSD) diagnosed after ischaemic stroke predicts recurrent ischaemic stroke in long-term follow-up. Methods We included 486 consecutive patients with ischaemic stroke (388 with first-ever stroke) admitted to Helsinki University Central Hospital who were followed-up for 12 years. Dementia was diagnosed in 115 patients using the Diagnostic and Statistical Manual of Mental Disorders, 3rd edition (DSM-III) criteria. The effects of risk factors and PSD on survival free of recurrent stroke were estimated using Kaplan–Meier log-rank analyses, and the HRs for stroke recurrence were calculated using Cox proportional hazards models. Results In the entire cohort, patients with PSD had a shorter mean time to recurrent stroke (7.13 years, 95% CI 6.20 to 8.06) than patients without dementia (9.41 years, 8.89 to 9.92; log rank p<0.001). This finding was replicated in patients with first-ever stroke (6.89 years, 5.85 to 7.93 vs 9.68 years, 9.12 to 10.24; p<0.001). In Cox univariate analysis, PSD was associated with increased risk for recurrent stroke both in the entire cohort (HR 2.02; 95% CI 1.47 to 2.77) and in those with first-ever stroke (2.40; 1.68 to 3.42). After adjustment for the significant covariates of age, atrial fibrillation, peripheral arterial disease and hypertension, PSD was associated with increased risk for recurrent stroke both in the entire cohort (1.84; 1.34 to 2.54) and in those with first-ever stroke (2.16; 1.51 to 3.10). Conclusions Poststroke dementia predicts recurrence of ischaemic stroke in long-term follow-up and should be considered when estimating prognosis.