Miracle-dz/UniFAR-FTUs huggingface dataset:
A Class of Algorithms for General Instrumental Variable Models

Causal treatment effect estimation is a key problem that arises in a variety of real-world settings, from personalized medicine to governmental policy making. There has been a flurry of recent work in machine learning on estimating causal effects when one has access to an instrument. However, to achieve identifiability, they in general require one-size-fits-all assumptions such as an additive error model for the outcome. An alternative is partial identification, which provides bounds on the causal effect. Little exists in terms of bounding methods that can deal with the most general case, where the treatment itself can be continuous. Moreover, bounding methods generally do not allow for a continuum of assumptions on the shape of the causal effect that can smoothly trade off stronger background knowledge for more informative bounds. In this work, we provide a method for causal effect bounding in continuous distributions, leveraging recent advances in gradient-based methods for the optimization of computationally intractable objective functions. We demonstrate on a set of synthetic and real-world data that our bounds capture the causal effect when additive methods fail, providing a useful range of answers compatible with observation as opposed to relying on unwarranted structural assumptions.
The Prevalence of Neuropsychiatric Disorders in a Nursing Home Population

The prevalence of neuropsychiatric disorders and other medical illnesses was investigated in 65 nursing home residents. The authors found neuropsychiatric disorders to be present in 94% of the sample. The neuropathologic causes of these syn dromes were found to be more diverse than in previous studies. The most frequent causes were degenerative, vascular, and toxic. The most common psychiatric syndromes that resulted from these neuropathologic disorders were dementia syndrome (72%), organic personality syndrome (14%), and organic psychotic disorders (12%). The most common behavioral prob lems, agitation and aggression, most likely reflected the high prevalence of frontal lobe damage and affected 48% of the sample. Other non-neuropsychiatric medical problems were significantly less common. While only 4% of the sample had no neuropsychiatric diagnosis, 39% had no other non-neuropsychiatric diagnosis. These results suggest that the nursing home is not used as a referral source for chronic medical conditions in general but almost exclusively for the care of chronic neuropsychiatric disorders. (J Geriatr Psychiatry Neurol 1988;1:71-76).
Intradiscal Pressure Measurements Above an Instrumented Fusion: A Cadaveric Study

Study Design. An in vitro study to determine the intradiscal pressure changes during flexion in levels above a simulated fusion was performed. Objectives. To determine if intradiscal pressure increases more during flexion in discs above an instrumented spinal segment compared to an uninstrumented segment. Summary of Background Data. The progressive degeneration of intervertebral discs adjacent to a fused or fixed segment is a phenomenon that is noted but poorly understood. Intuitively, the degeneration appears to be a function of altered biomechanics of the motion segments in the spine. Methods. Two intervertebral disc levels were evaluated, L3-L4 and L4-L5 from each of six fresh frozen cadaver spines. Pressure measurements were taken with the spine uninstrumented, with bilateral pedicle screw-rod instrumentation from L5 to S1, and with bilateral pedicle screw-rod instrumentation from L4to S1. Pressure measurements were accomplished with Millar Mikro-Tip pressure transducers. The transducers were placed within the nucleus pulposus of L3-L4 and L4-L5 intervertebral discs. Pressure data were recorded by computer data acquisition. The pressure data were compared by intervertebral level and by the effects of added instrumentation. Results. In general, the addition of instrumentation significantly affected the intradiscal pressure in the levels above a simulated fusion. The intradiscal pressure increased as the amount of levels involved in the simulated fusion increased. The intradiscal pressure increased as flexion motion increased. A greater increase was seen at the L4-L5 level than the L3-L4 level. When L5-S1 fixation was added, the intradiscal pressure increased. When L4-S1 fixation was added, the intradiscal pressure further increased.
Virtual Movements Activate Primary Sensorimotor Areas in Amputees: Report of Three Cases

OBJECTIVEIn our multidisciplinary pain clinic, three patients with amputated limbs and with surgical indications for chronic motor cortex stimulation for phantom limb pain were selected for their ability to voluntarily move the missing limb. The sensation of being able to move a missing limb at will occurs quite frequently among traumatic amputees, but the ability to control it sufficiently to perform a functional magnetic resonance imaging (fMRI) examination is more rarely encountered. We used motor fMRI to study these virtual movements. METHODSIn two patients with upper-limb amputations, movements of the stump, the normal hand, and the missing arm were studied. In a third patient with both legs amputated, movements of the stumps and of the missing feet were studied. The fMRI data were analyzed with the Statistical Parametric Map 96 software and reformatted for integration into anatomic slices. RESULTSVirtual movements of the missing limbs produced contralateral primary sensorimotor cortex and central sulcus activations in the patients with upper-limb amputation. Interhemispheric and bilateral activations were found in the patient with both legs amputated. These activation areas were different from the stump activation areas. Additionally, the significance thresholds chosen to generate the activation maps in virtual movements (although individual) were globally the same as those used to detect motor activation in the normal side of the patients. CONCLUSIONCortical areas devoted to the missing limb seem to persist for several years after amputation. The precentral activations found in our patients are in agreement with the statement that the neural mechanisms involved in the mental representation of an action and in its execution are the same. Data from fMRI can be used to evaluate phantom limb virtual movements and to study cortical reorganization phenomena that can appear with time or as a result of some therapies. In these patients, fMRI data may be useful in assisting the neurosurgeon in the placement of chronic motor cortex electrodes.
Flux Limitations of Continuous Atom Lasers

If atom lasers are to transform many fields of physics, as well as find applications in industry, the most essential development needed is increased atom flux. In this thesis we report on the experimental observation of fundamental limits on the flux of continuous atom lasers. The flux produced by the commonly used radio frequency outcoupler, can not be arbitrarily increased by increasing the strength of the outcoupling. Above a critical Rabi frequency, the atom laser shows large classical density fluctuations, due to coupling between the multiple Zeeman states. In our system this critical Rabi frequency is ∼ 1 kHz. Futhermore, at large coupling strengths (> 4 kHz for our experimetnal parameters), the continuous atom laser output completely switches off, as a result of the atoms remaining trapped in a bound state. In addition to the investigations of the radio frequency outcoupler, we have demonstrated the first continuous Raman outcoupled atom laser. Preliminary data indicates that the Raman outcoupler will be flux limited in a similar way to the radio frequency outcoupler.
RNA-Dependent Cysteine Biosynthesis in Archaea

Several methanogenic archaea lack cysteinyl–transfer RNA (tRNA) synthetase (CysRS), the essential enzyme that provides Cys-tRNACys for translation in most organisms. Partial purification of the corresponding activity from Methanocaldococcus jannaschii indicated that tRNACys becomes acylated with O-phosphoserine (Sep) but not with cysteine. Further analyses identified a class II–type O-phosphoseryl-tRNA synthetase (SepRS) and Sep-tRNA:Cys-tRNA synthase (SepCysS). SepRS specifically forms Sep-tRNACys, which is then converted to Cys-tRNACys by SepCysS. Comparative genomic analyses suggest that this pathway, encoded in all organisms lacking CysRS, can also act as the sole route for cysteine biosynthesis. This was proven for Methanococcus maripaludis, where deletion of the SepRS-encoding gene resulted in cysteine auxotrophy. As the conversions of Sep-tRNA to Cys-tRNA or to selenocysteinyl-tRNA are chemically analogous, the catalytic activity of SepCysS provides a means by which both cysteine and selenocysteine may have originally been added to the genetic code.
Anopheles gambiae (Diptera: Culicidae) Oviposition in Response to Agarose Media and Cultured Bacterial Volatiles

Abstract Anopheles gambiae s.s. Giles accepted a range of agarose gels, varying from 0.5 to 8% (wt:vol), for oviposition; laid more eggs on 0.5% agarose gels than on moist filter paper or on drier agarose; and laid equal numbers of eggs on 0.5% agarose gels and distilled water. Larvae hatched on agarose gel substrates and crawled onto the surface of moist agarose gels, but they tended only to burst the egg cap and remain within the egg case on drier gels. A mixture of cultured bacteria, originating from a natural larval habitat of An. gambaiae s.s. in western Kenya, was classified by 16S rDNA sequence analysis, and then this mixture or individual colonies from it was used as odor sources in ovipositional experiments with agarose substrates. Of 61 sequences from a mixed clone sequence library, most (78%) were Pseudomonas strains, whereas the remainder were Stenotrophomonas, Enterobacter, Pantoea, Klebsiella, Acinetobacter, Aeromonas, and Bacillus. Oviposition was significantly reduced when mixtures of bacterial colonies of these strains, or a lawn of colonies of a field isolate of S. maltophilia, was presented. Oviposition was neither reduced nor enhanced when field isolates of Pseudomonas putida or Pseudomonas alcaligenes colonies were presented. These results suggest that gravid An. gambiae females are sensitive to bacterial-derived odors emanating from cultured bacteria from natural larval habitats and that some bacterial odors may be repellent.
Synchronization of heterogeneous agents using min-max optimization

In this paper, we address the problem of output synchronization of networks of non-identical linear time-invariant agents. Relying on the notion of the internal-reference principle for synchronization, we propose a dynamic output feedback controller for every agent to solve the problem at hand. We emphasize the fact that the distributed controllers are only driven by relative output information and thus the communication load for the network is minimized. Furthermore, a min-max optimization algorithm is provided allowing to determine suitable controller parameters for each agent such that all outputs synchronize asymptotically. The results are illustrated by a numerical example.
Thyrotoxicosis in Pregnancy Presenting as Pancytopenia

EDITORIAL COMMENT: In spite of its rarity we accepted this case report for presentation to remind readers of the dire complications that can occur in a woman with thyrotoxicosis that has escaped recognition. It is a reminder that thyroid function should be tested in patients who present with severe medical emergencies of uncertain aetiology.
Lipoxin A4 stimulates endothelial miR‐126–5p expression and its transfer via microvesicles

The proresolution lipid mediator lipoxin (LX)A4 bestows protective bioactions on endothelial cells. We examined the impact of LXA4 on transcellular endothelial signaling via microRNA (miR)‐containing microvesicles. We report LXA4 inhibition of MV release by TNF‐α‐treated HUVECs, associated with the down‐regulation of 18 miR in endothelial microvesicles (EMVs) and the up‐regulation of miR‐126–5p, both in HUVECs and in EMVs. LXA4 upregulated miR‐126–5p by ∼5‐fold in HUVECs and promoted a release of microvesicles (LXA4‐EMVs) that enhanced miR‐126–5p by ∼7‐fold in recipient HUVECs. In these cells, LXA4‐EMVs abrogated the up‐regulation of VCAM‐1, induced in recipient HUVECs by EMVs released by untreated or TNF‐α‐treated HUVECs. LXA4‐EMVs also reduced by ∼40% the expression of SPRED1, which we validated as an miR‐126–5p target, whereas they stimulated monolayer repair in an in vitro wound assay. This effect was lost when the EMVs were depleted of miR‐126–5p. These results provide evidence that changes in miR expression and microvesicle packaging and transfer represent a mechanism of action of LXA4, which may be relevant in vascular biology and inflammation. —Codagnone, M. , Recchiuti, A. , Lanuti, P., Pierdomenico, A. M. , Cianci, E. , Patruno, S. , Mari, V. C. , Simiele, F. , Di Tomo, P., Pandolfi, A. , Romano, M. Lipoxin A4 stimulates endothelial miR‐126–5p expression and its transfer via microvesicles. FASEB J. 31, 1856–1866 (2017). www.fasebj. org
Evaluation of Pure Tone and Speech Discrimination Changes in Usher's Syndrome

Twenty-three adult patients with type 2 Usher's syndrome were evaluated for changes in pure tone average (PTA), discrete frequency thresholds, and speech discrimination scores. These patients were evaluated over a period of 5 years on the average (range, 2 to 9 years). Analyses of ear data showed a <10-dB change on PTA and discrete frequency thresholds for most ears. Of the ears that showed a threshold change ≥ 10 dB, statistical significance was reached only at 4,000 Hz (p < .01), where 11 ears representing ten patients dropped 10 to 15 dB. Speech discrimination data showed a ≥ 16% change in score for 18 ears (12 patients). Sixteen of those ears (ten patients) had a 16% to 52% decrease in score (p < .01), and the remaining two ears (two patients) showed a 20% and 30% improvement in score. These findings document little or no change in pure tone sensitivity for type 2 Usher's syndrome patients, but demonstrate the importance of monitoring their speech discrimination performance.
Nandrolone and stanozolol induce leydig cell tumor proliferation through an estrogen‐dependent mechanism involving IGF‐I system

Several substances such as anabolic androgenic steroids (AAS), peptide hormones like insulin‐like growth factor‐I (IGF‐I), aromatase inhibitors and estrogen antagonists are offered via the Internet, and are assumed without considering the potential deleterious effects that can be caused by their administration. In this study we aimed to determine if nandrolone and stanozolol, two commonly used AAS, could have an effect on Leydig cell tumor proliferation and if their effects could be potentiated by the concomitant use of IGF‐I. Using a rat Leydig tumor cell line, R2C cells, as experimental model we found that nandrolone and stanozolol caused a dose‐dependent induction of aromatase expression and estradiol (E2) production. When used in combination with IGF‐I they were more effective than single molecules in inducing aromatase expression. AAS exhibited estrogenic activity and induced rapid estrogen receptor (ER)‐dependent pathways involving IGF1R, AKT, and ERK1/2 phosphorylation. Inhibitors for these kinases decreased AAS‐dependent aromatase expression. Up‐regulated aromatase levels and related E2 production increased cell proliferation as a consequence of increased cyclin E expression. The observation that ER antagonist ICI182,780 was also able to significantly reduce ASS‐ and AAS + IGF‐induced cell proliferation, confirmed a role for estrogens in AAS‐dependent proliferative effects. Taken together these data clearly indicate that the use of high doses of AAS, as it occurs in doping practice, enhances Leydig cell proliferation, increasing the risk of tumor development. This risk is higher when AAS are used in association with IGF‐I. To our knowledge this is the first report directly associating AAS and testicular cancer. J. Cell. Physiol. 227: 2079–2088, 2012. © 2011 Wiley Periodicals, Inc.
TheolsAgenemediates the synthesis ofanornithine lipid in Pseudomonasaeruginosaduringgrowthunderphosphate-limiting conditions , but is not involved inantimicrobial peptide susceptibility

TheolsAgenemediates the synthesis ofanornithine lipid in Pseudomonasaeruginosaduringgrowthunderphosphate-limiting conditions, but is not involved inantimicrobial peptide susceptibility Shawn Lewenza, Reza Falsafi, Manjeet Bains, Patricia Rohs, Jacek Stupak, G. Dennis Sprott & Robert E.W. Hancock Department of Microbiology and Infectious Diseases, Health Sciences Centre, University of Calgary, Calgary, AB, Canada; Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada; and Institute for Biological Sciences, National Research Council, Ottawa, ON, Canada
Palliative Chemotherapy Affects Aggressiveness of End-of-Life Care.

INTRODUCTION Although palliative chemotherapy during end-of-life care is used for relief of symptoms in patients with metastatic cancer, chemotherapy may lead to more aggressive end-of-life care and less use of hospice service. This is a population-based study of the association between palliative chemotherapy and aggressiveness of end-of-life care. PATIENTS AND METHODS Using the National Health Insurance Research Database of Taiwan, we identified 49,920 patients with metastatic cancer who underwent palliative chemotherapy from January 1, 2009, to December 31, 2011. Patients who received chemotherapy 2-6 months before death were included. Aggressiveness of end-of-life care was examined by previously reported indicators. Cardiopulmonary resuscitation and endotracheal tube intubation were included as indicators of aggressive end-of-life care. The association between palliative chemotherapy and hospice care was studied. RESULTS Palliative chemotherapy was associated with more aggressive treatment. After adjustment for patient age, sex, Charlson Comorbidity Index score, cancer group, primary physician's specialty, postdiagnosis survival, hospital characteristics, hospital caseload, urbanization, and geographic regions, more than one emergency room visit (p < .001), more than one intensive care unit admission (p < .001), and endotracheal intubation (p = .02) during end-of-life care were significantly more common in patients receiving palliative chemotherapy. Patients who did not receive palliative chemotherapy received more hospice care in the last 6 months of life (p < .001). CONCLUSION Although the decision to initiate palliative chemotherapy was made several months before death, this study showed that palliative chemotherapy was associated with more aggressive end-of-life care, including more emergency room visits and intensive care unit admissions, and endotracheal intubation. The patients who received palliative chemotherapy received less hospice service toward the end of life. IMPLICATIONS FOR PRACTICE Palliative chemotherapy is used for patients with incurable cancer toward the end of life (EOL). Aggressiveness of EOL care and hospice care are related to the quality of life of these patients. This study of data from the Taiwanese National Health Insurance Research Database found that palliative chemotherapy led to more aggressive EOL care and less hospice care. There is a need to provide patients with terminal cancer access to care information that best meets their needs, especially those patients who receive palliative chemotherapy.
Small cell melanoma

Malignant melanoma is one of the great mimics in human pathology: many examples cause no great diagnostic dif®culty but at the two boundaries, ®rst, with benign naevi and, second, with other highgrade malignancies, there is plenty of room for confusion. Small cell melanoma is a variant of melanoma that is relevant to both of these situations. This is a possible source of confusion. The term `small cell carcinoma' is widely used in pathology. The most common context is the small cell, or oat cell, carcinoma of the bronchus, with which we are familiar and which is recognized as a high-grade malignancy with a typical `small blue cell' appearance. These tumours usually show necrosis, atypical mitoses and apoptosis. Similar tumours are seen in various other organs around the body and show an overlap with the Merkel cell neuroendocrine carcinoma of the skin. Some melanomas fall into this category. More confusingly, `small cell carcinoma' has been used to describe some other tumour entities with quite different appearances from the archetype in the bronchus. Small cell carcinoma of the ovary (with hypercalcaemia) is an example. In the context of small cell melanoma there is a subset of tumours that have architectural and cytological features that overlap with benign melanocytic naevi. In this issue of Histopathology, Hanson et al. describe 11 examples to illustrate the problem and emphasize that although the two varieties of small cell melanoma can be recognized, there is considerable overlap and indeed they probably represent ends of a relatively short spectrum. Small cell melanoma mimicking benign melanocytic naevus
Modeling African American prostate adenocarcinoma by inducing defined genetic alterations in organoids

Genomic studies are rapidly identifying genetic alterations in human cancer, but functional validation of such alterations has been slow. Here, using human prostate cancer as a model, we have assessed the feasibility of engineering defined genetic alterations in well-known cancer driver genes to transform benign prostate epithelial organoids derived from African American men. Benign human prostate organoids were transduced with lentiviruses expressing MYC, shPTEN, shTP53 and AR, alone and in various combinations, to recapitulate prostate cancer development. Organoids expressing MYC, shPTEN, shTP53 and AR (denoted MPPA); MYC, shPTEN and shTP53 (MPP); or MYC (M) were significantly larger, had higher proliferation rates and demonstrated pathologically transformed morphology compared to organoids transduced with control lentivirus. Alterations in MYC, PTEN and TP53 also affected the rate of organoid basal-to-luminal differentiation in vitro. MPPA and MPP organoids expressed the clinical prostate cancer marker AMACR and developed prostate adenocarcinoma when grafted under the renal capsule in mice. These data indicate that genetic alterations commonly observed in human prostate cancer can be rapidly modeled in human organoid culture. Prostate cancer organoids provide a useful pre-clinical model for the evaluation of new candidate cancer genes, cancer disparities, and potentially for testing of novel therapeutic agents.
Quantitative evaluation of parenchymal liver cell volume and total hepatocyte number in cirrhotic patients

A simple morphometrical method was developed using a color image analyzing system, which allowed quantitative evaluation of parenchymal liver cell volume and total hepatocyte number in cirrhotic patients. With this method, we estimated these values in 29 cirrhotic patients who underwent hepatic resection (nine cases) or nonshunting operation (20 cases). Liver volume, calculated from computed tomographic images, was 976 ± 196 cm3 (range = 602 to 1,376 cm3); the parenchymal cell volume ratio, obtained based on liver histological appearance with silver stain, was 0.665 ± 0.092 (range = 0.510 to 0.881); and the parenchymal cell volume, calculated by multiplying the liver volume with the parenchymal cell volume ratio, was 645 ± 140 cm3 (range = 403 to 936 cm3). The total hepatocyte number obtained in a similar manner using hematoxylin‐stained specimens was 1.72 ± 0.56 × 1011 (range = 0.74 to 2.94 × 1011). The validity and applicability of the method is discussed, and the data are compared with those reported in other studies.